Exactive Software Manual Rev.C

Exactive Software Manual Rev.C
Thermo Fisher Scientific
™
Exactive
Software Manual
Revision C - 1249910
Part of Thermo Fisher Scientific
© 2011 Thermo Fisher Scientific Inc. All rights reserved.
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Fisher Scientific Inc.
The contents of this document are subject to change without notice. All technical information in this
document is for reference purposes only. System configurations and specifications in this document
supersede all previous information received by the purchaser.
Thermo Fisher Scientific Inc. makes no representations that this document is complete, accurate
or error-free and assumes no responsibility and will not be liable for any errors, omissions,
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Release History: Revision A released in January 2009
Revision B released in July 2009
Revision C released in December 2011
Software Version: Exactive Tune 1.1 SP5
For Research Use Only. Not for use in diagnostic procedures.
Read This First
Welcome to the Thermo Scientific Exactive system! Exactive™ is a
member of the Thermo Scientific family of mass spectrometer (MS)
detectors that are powered by Orbitrap™ technology.
About This Guide
This Exactive Software Manual provides reference information about the
parameters in the Instrument Configuration window, the Instrument
Setup window, and the Exactive Tune window. For information about
the operating procedures for the Exactive mass spectrometer, we
recommend that you read the Exactive Operating Manual in its entirety.
Who Uses This Guide
This Exactive Software Manual is intended for all personnel that need to
perform measurements with the Exactive mass spectrometer, especially
the key operator. This manual should be kept near the instrument to be
available for quick reference.
Scope of This Guide
The Exactive Software Manual includes the following chapters:
• Chapter 1: “Instrument Configuration Window” describes the
Exactive Configuration window, which displays configuration
information.
• Chapter 2: “Exactive Readback Status Page for the Information
View” describes the page that allows controlling the instrument
from the Roadmap view of the Xcalibur Home Page window.
• Chapter 3: “Instrument Setup” describes Instrument Setup, which is
used to specify instrument settings.
• Chapter 4: “Explore Exactive Tune” provides information about
Exactive Tune, its views, functions, and features.
• Chapter 5: “Procedures in Exactive Tune” provides information
about procedures in Exactive Tune.
• Chapter 6: “Reference Information” provides information about
various file types.
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Exactive Software Manual (P/N 1249910, Revision C)
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Read This First
About This Guide
Related Documentation
In addition to this guide, Thermo Fisher Scientific provides the
following documents for the Exactive mass spectrometer:
• Exactive Series Preinstallation Requirements Guide
• Exactive QuickStart Guide
• Exactive Operating Manual
• Manuals for the delivered ion sources and other software.
You can access PDF files of the documents listed above from the data
system computer. The Exactive Tune software also provides Help.
❖
To view product manuals
Go to Start > Programs > Thermo Exactive > Manuals.
❖
To open Help
• From the Exactive Tune window, choose Help > Help Content.
• If available for a specific window or dialog box, click Help or press
F1 for information about setting parameters.
For more information, including upcoming application notes, visit
www.thermoscientific.com.
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Read This First
Contacting Us
Contacting Us
There are several ways to contact Thermo Fisher Scientific.
Assistance
For technical support and ordering information, visit us on the Web:
www.thermoscientific.com/ms
Service contact details are available under:
www.unitylabservice.com
Customer Information Service
cis.thermo-bremen.com is the Customer Information Service site aimed
at providing instant access to
• latest software updates
• manuals, application reports, and brochures.
Note Thermo Fisher Scientific recommends that you register with the
site as early as possible. ▲
To register visit register.thermo-bremen.com/form/cis and fill in the
registration form. Once you registration has been finalized you will
receive confirmation by e-mail.
Changes to the Manual
❖
To suggest changes to this manual
•
Please send your comments (in German or English) to:
Editors, Technical Documentation
Thermo Fisher Scientific (Bremen) GmbH
Hanna-Kunath-Str. 11
28199 Bremen
Germany
•
Send an e-mail message to the Technical Editor at
[email protected]
You are encouraged to report errors or omissions in the text or index.
Thank you.
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Read This First
Typographical Conventions
Typographical Conventions
This section describes typographical conventions that have been
established for Thermo Fisher Scientific manuals.
Data Input
Throughout this manual, the following conventions indicate data input
and output via the computer:
• Messages displayed on the screen are represented by capitalizing the
initial letter of each word and by italicizing each word.
• Input that you enter by keyboard is identified by quotation marks:
single quotes for single characters, double quotes for strings.
• For brevity, expressions such as “choose File > Directories” are used
rather than “pull down the File menu and choose Directories.”
• Any command enclosed in angle brackets < > represents a single
keystroke. For example, “press <F1>” means press the key labeled
F1.
• Any command that requires pressing two or more keys
simultaneously is shown with a plus sign connecting the keys. For
example, “press <Shift> + <F1>” means press and hold the <Shift>
key and then press the <F1> key.
• Any button that you click on the screen is represented in bold face
letters. For example, “click Close”.
Topic Headings
The following headings are used to show the organization of topics
within a chapter:
Chapter 1
Chapter Name
Second Level Topics
Third Level Topics
Fourth Level Topics
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Read This First
Safety and Special Notices
Safety and Special Notices
Read and understand the various precautionary notes, signs, and
symbols contained inside this manual pertaining to the safe use and
operation of this product before using the device.
Make sure you follow the precautionary statements presented in this
guide. The safety and other special notices appear different from the
main flow of text. Safety and special notices include the following:
Warning Warnings highlight hazards to human beings. Each Warning is
accompanied by a Warning symbol. ▲
Caution Cautions highlight information necessary to protect your
instrument from damage. ▲
Note Notes highlight information that can affect the quality of your
data. In addition, notes often contain information that you might need
if you are having trouble. ▲
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Safety and Special Notices
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Contents
Thermo Fisher Scientific
Chapter 1
Instrument Configuration Window ........................................1-1
Chapter 2
Exactive Readback Status Page for the Information
View.............................................................................................2-1
Chapter 3
Instrument Setup .......................................................................3-1
Instrument Setup Window................................................ 3-2
File Menu for the Instrument Setup Window ................ 3-3
Help Menu for the Instrument Setup Window .............. 3-5
Instrument Setup Window Toolbar ............................... 3-5
Exactive Instrument Setup - New Method Page ............. 3-7
MS Detector Setup Page ................................................... 3-8
Scan Event Table ......................................................... 3-12
Locking Dialog Box of the MS Detector Setup Page .... 3-17
Syringe Pump Page ......................................................... 3-21
Divert Valves Page .......................................................... 3-25
Contact Closure Page...................................................... 3-28
Summary Page ................................................................ 3-31
Chapter 4
Explore Exactive Tune .............................................................4-1
Exactive Tune Overview ................................................... 4-2
Exactive Tune Menus........................................................ 4-5
File Menu ...................................................................... 4-5
Windows Menu ............................................................. 4-5
Reports Menu ................................................................ 4-6
Help Menu .................................................................... 4-7
Toolbar ............................................................................. 4-8
Tasks Panel ..................................................................... 4-11
Instrument Control Window ....................................... 4-11
Tune Window ............................................................. 4-42
Calibrate Window........................................................ 4-44
Evaluate Window......................................................... 4-46
Vacuum / Bakeout Window......................................... 4-47
Display Panel .................................................................. 4-50
Spectrum Window ....................................................... 4-51
Instrument Status Window .......................................... 4-54
Messages Window........................................................ 4-55
Analysis Graphs Window ............................................. 4-56
Debug Messages Window ............................................ 4-58
Dialog Boxes ................................................................... 4-61
About Dialog Box ........................................................ 4-62
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Contents
License Dialog Box ...................................................... 4-63
Syringe Pump Settings Dialog Box............................... 4-64
Scan Parameters History Dialog Box............................ 4-66
Scan Range Dialog Box ................................................ 4-66
Fragmentation Dialog Box ........................................... 4-68
Collection Modification Dialog Box ............................ 4-70
Lock Masses Dialog Box .............................................. 4-71
Lock Mass Removal Dialog Box................................... 4-74
Lock Mass Replacement Dialog Box ............................ 4-75
New Lock Mass Collection Dialog Box........................ 4-75
Delete Lock Mass Collection Dialog Box ..................... 4-76
Name Change Dialog Box ........................................... 4-77
Display Options Dialog Box ........................................ 4-78
Chapter 5
Procedures in Exactive Tune ................................................. 5-1
Using Lock Masses and Lock Mass Collections ................. 5-2
Adding a Lock Mass....................................................... 5-2
Deleting Lock Masses..................................................... 5-3
Exporting and Importing Lock Masses........................... 5-3
Creating a new Lock Mass Collection .......................... 5-11
Renaming a Lock Mass Collection ............................... 5-11
Adding a Lock Mass to a Lock Mass Collection ........... 5-12
Removing a Lock Mass from a Lock Mass
Collection .................................................................... 5-12
Deleting a Lock Mass Collection.................................. 5-12
Performing a System Bakeout.......................................... 5-13
Changing Default Settings of Exactive Tune ................... 5-15
Displaying the High Vacuum Readback....................... 5-15
Calibrating with Custom Mass Lists............................. 5-16
Entering Parameters for the Syringe Pump................... 5-20
Changing the Settings for the Performance Status
Check .......................................................................... 5-21
Chapter 6
Reference Information............................................................. 6-1
Log Files ........................................................................... 6-2
Tune Files and Calibration Files........................................ 6-3
Glossary .................................................................................... G-1
Index ............................................................................................ I-1
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Figures
Instrument Configuration window ........................................................ 1-1
Exactive Readback Status Page for the Information View ...................... 2-1
Instrument Setup window ..................................................................... 3-2
New Method page of Exactive Instrument Setup window ..................... 3-7
MS Detector Setup page ....................................................................... 3-8
Scan Event table of the MS Detector Setup page ................................. 3-12
Scan range dialog box of the MS Detector Setup page ......................... 3-14
Fragmentation dialog box of the MS Detector Setup page .................. 3-16
Locking Dialog Box of the MS Detector Setup page ........................... 3-17
Syringe Pump page ............................................................................. 3-21
Divert Valves page ............................................................................... 3-25
Contact Closure page .......................................................................... 3-28
Summary page .................................................................................... 3-31
Exactive Tune ....................................................................................... 4-2
Scan Parameters window ..................................................................... 4-12
ESI source window .............................................................................. 4-15
HESI source window .......................................................................... 4-19
NSI source window ............................................................................. 4-24
APCI source window .......................................................................... 4-28
APPI source window ........................................................................... 4-33
Acquisition window ............................................................................ 4-38
Tune window ...................................................................................... 4-42
Calibrate window ................................................................................ 4-44
Evaluate window ................................................................................. 4-46
Vacuum / Bakeout window ................................................................. 4-47
Spectrum window ............................................................................... 4-51
Instrument Status window .................................................................. 4-54
Messages window ................................................................................ 4-55
Analysis Graphs window ..................................................................... 4-56
Debug Messages window .................................................................... 4-58
About dialog box ................................................................................. 4-62
License dialog box ............................................................................... 4-63
Syringe Pump Settings dialog box ....................................................... 4-64
Scan Parameters History dialog box .................................................... 4-66
Scan range dialog box .......................................................................... 4-66
Tune – Fragmentation dialog box ....................................................... 4-68
Collection Modification dialog box ..................................................... 4-70
Tune – Lock Masses dialog box ........................................................... 4-71
Lock Mass Removal dialog box ........................................................... 4-74
Lock Mass Replacement dialog box ..................................................... 4-75
New Lock Mass Collection dialog box ................................................ 4-75
Delete Lock Mass Collection dialog box .............................................. 4-76
Name Change Dialog Box .................................................................. 4-77
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Figures
Display Options Dialog Box ............................................................... 4-78
Adding a new lock mass ........................................................................ 5-2
Selecting the lock mass export file ......................................................... 5-5
Selecting the lock mass export file ......................................................... 5-6
Selecting the lock mass import file ........................................................ 5-8
Selecting the lock mass import file ...................................................... 5-10
Creating a lock mass collection ............................................................ 5-11
Changing the name of a lock mass collection ...................................... 5-11
Vacuum / Bakeout window ................................................................. 5-13
Bakeout message box ........................................................................... 5-14
Message box: Vacuum Bakeout active ................................................. 5-14
Instrument status window – User Mass List node ................................ 5-16
Editing a user-defined mass list ........................................................... 5-17
Instrument status window – Calibrate node ........................................ 5-19
Selecting a custom mass list for calibration .......................................... 5-19
Instrument status window – Peripherals node ..................................... 5-20
Instrument status window – Performance Check node ........................ 5-21
Changing the calibration validity period .............................................. 5-22
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Chapter 1
Instrument Configuration Window
Caution Never change the settings in this window except during
installation of the instrument. Any changes in this window affect the
data acquisition or the functionality of your instrument. A later change
will rarely solve problems users have to face. ▲
The Exactive Configuration window displays Exactive configuration
information. See Figure 1-1.
Figure 1-1.
Instrument Configuration window
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1-1
Instrument Configuration Window
The Instrument Configuration window has the following parameters:
Parameter
Description
Path to instrument files
Displays the location of the instrument
files.
To change the path, use the folder button
on the right side of the text box. In a dialog
box, you can then select another location.
Path to log files
Displays the location of the log files. For
information about the content of the log
files, see “Log Files” on page 6-2.
To change the path, use the folder button
on the right side of the text box. In a dialog
box, you can then select another location
Base port
Displays the first TCP/UDP port in use for
this particular instrument. Leave the field
empty for an automatic assignment.
Network address
Displays the hardware address of the
network card installed in the instrument.
Leave the field empty for an automatic
assignment.
IP address
Displays the IP address. Leave the field
empty for an automatic assignment.
Public Name
Displays the name that is shown in the
About dialog box of Exactive Tune.
IP address range
Displays the IP address or IP address range
which should be assigned to the instrument
during its starting phase. Use the numeric
form, e.g. “127.2.123.1” or
“172.16.2.1-172.16.2.15”.
Note Change only when advised by your
network administrator. ▲
Message box
Displays information about the instrument
and connection status.
Buttons
1-2
Apply
Saves your changes in this window.
Reset changes
Discards your changes in this window.
Help
Displays the Help for this window.
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Instrument Configuration Window
❖
To display this window
1. Choose Programs > Thermo Foundation 1.0 > Instrument
Configuration.
2. From the Instrument Configuration window, click Exactive Orbitrap MS in the Configured Devices area.
3. Click Configure.
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Instrument Configuration Window
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Exactive Readback Status Page for the
Information View
Chapter 2
The readback status of each Xcalibur-configured instrument appears on
the Status page of the Information view. When you click an instrument,
Xcalibur displays current readings for the instrument on a page below
the Run Manager pane. See Figure 2-2.
Right-click any of the instruments to display a shortcut menu where you
can switch your instrument to On, Off, or Standby mode.
Note This view is normally displayed on the left side of the Home Page
window. If this view is not displayed, the view has been turned off. ▲
Figure 2-2.
Thermo Fisher Scientific
Exactive Readback Status Page for the Information View
Exactive Software Manual (P/N 1249910, Revision C)
2-1
Exactive Readback Status Page for the Information View
The following functions are available:
Button
Description
Communication Status
Shows the actual communication status of the system:
• Green: communication with instrument is ok.
• Yellow: only service is accessible (no instrument).
• Red: communication is broken (no instrument, no service).
Instrument Status
Shows the actual hardware status of the system (top instrument tree
state):
• Green: all readbacks are in specifications (green hooks).
• Red: one or more readbacks are out of range.
Performance Status
Shows the actual performance status of the system:
• Green: the last evaluation/calibration was successful.
• Yellow: last evaluation/calibration was successful, but is out of
date.
• Red: the evaluation/calibration was not successful.
Tune
Opens the Exactive Tune window.
❖
To open this page
1. From the Home Page window, choose View > Info View to display
the Information view.
2. Click the Status tab.
3. Click Exactive - Orbitrap MS.
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Chapter 3
Instrument Setup
After selecting which instruments you want Xcalibur to control using
the Instrument Configuration program, use Instrument Setup to specify
your instrument settings.
Contents
Thermo Fisher Scientific
•
Instrument Setup Window
•
MS Detector Setup Page
•
Syringe Pump Page
•
Divert Valves Page
•
Contact Closure Page
•
Summary Page
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Instrument Setup
Instrument Setup Window
Instrument Setup Window
The Instrument Setup window displays the icons of the instruments
that you have selected using the Instrument Configuration window. (See
the View bar on the left side of the window.) See Figure 3-3. If you have
configured more instruments than can be displayed on your screen, a
vertical scroll bar appears in the View bar so that you can access all of the
instruments.
Figure 3-3.
Instrument Setup window
To enter the setup parameters for a particular instrument, click the icon
for that instrument. Xcalibur displays one or more pages of parameters
to be set for the one you selected.
Note Prior to using the Instrument Setup window, use the Instrument
Configuration program to select the instruments to be used for your
experiment. ▲
Use Instrument Setup to specify settings for your instruments after you
have selected with the Instrument Configuration program which
instruments you want Xcalibur to control. The Instrument Setup
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Instrument Setup
Instrument Setup Window
window displays the setup parameters required for each instrument that
you select on the View bar. These might include your autosampler,
chromatograph, mass spectrometer, divert valves, syringe pump, contact
closure timing sequence, and/or all other Xcalibur supported
instruments that you have configured.
You can create new methods, modify existing methods, and save method
files.
You can also enter a method summary that appears in the Open dialog
box and on all method printouts. All changes are audited by logon ID
and user self-identification so that you can describe why you changed a
method.
❖
To display this window
Click
from the Roadmap view of the Home Page window.
Alternatively, choose GoTo > Instrument Setup.
View Bar
The View bar is a vertical bar on the left of the Instrument Setup
window. It contains buttons for each of the instruments that you have
selected by using the Instrument Configuration program.
Menus
Instrument Setup contains the following menus:
•
File Menu for the Instrument Setup Window
•
Help Menu for the Instrument Setup Window
Toolbar
Instrument Setup Window Toolbar
File Menu for the Instrument Setup Window
The File menu provides commands for file and program operations. It
has the following commands:
Thermo Fisher Scientific
Command
Description
New
Create a new method file having the
appropriate extension.
Open
Find and open a file that already exists.
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Instrument Setup
Instrument Setup Window
Command
Description
Save
Open the File Save - Audit Trail dialog box if
the file has been saved before so that you can
enter audit information about the active file.
Save As
Edit user and description information, as well
as view header information about the active
file.
When you click OK, Xcalibur opens the File
Save - Audit Trail dialog box, so you can enter
audit information about the active file. When
you click Continue, Xcalibur saves the file.
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Summary
Information
Edit user and description information, as well
as view header information about the active
file.
Change Study
Name
Select a dataset from a predefined list of names.
Audit Trail
View all auditable events and changes made to
data files in the current application.
Print
Print the parameters in your instrument
method.
Print Preview
View your page setup so that you can see what
it looks like before printing it.
Print Setup
Select the following printing options: printer,
form, orientation, and one- or two-sided
printing.
Most Recently
Used Files
View the paths and names of the last four files
used. These are located above the Exit
command. Both open and closed files are
displayed. Click a displayed file to load it. If
the selected file was closed, it will be opened.
Exit
Close the active window. If you exit before
clicking OK from an active dialog box,
Xcalibur asks if you want to save your changes.
The text of this menu item might be different
if the administrator chose to use another name
for a dataset. For example, this menu item
might be Change Job Name.
Thermo Fisher Scientific
Instrument Setup
Instrument Setup Window
Help Menu for the Instrument Setup Window
The Help menu groups commands that provide information about the
Instrument Setup window. It has the following commands:
Command
Description
Exactive - Orbitrap MS
Help
Open the Configuration and Setup Help
for the instrument.
Instrument Setup Help
Open Xcalibur Help and display Help for
the Instrument Setup window.
Help On Current Item
View Help for the Instrument Setup page
that is currently displayed.
Exactive - Orbitrap MS
Contents and Index
View the Contents, Index, and Find Help
pages for the selected instrument.
Xcalibur Help
Open Xcalibur Help.
Glossary
Open the Xcalibur glossary.
How to use Online Help
Open Help that describes how to use the
Help viewer.
About Instrument Setup
View the version number of the
Instrument Setup program and the
Thermo Fisher Scientific copyright
notice.
Instrument Setup Window Toolbar
The toolbar provides symbol shortcuts for frequently used commands.
The following functions are available:
Thermo Fisher Scientific
Button
Description
New
Create a new instrument method.
Open
Find and open an existing file.
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Instrument Setup
Instrument Setup Window
Button
Description
Save
Enter audit information about the active file if
your method has been saved before and click
Continue to save the file.
If your method has not been saved before,
clicking Save opens the Save As dialog box. Select
the name and location for your instrument
method. When you click Save, the File Summary
Information Dialog Box opens. Enter header
information for your instrument method. When
you click OK, the File Save - Audit Trail Dialog
Box opens. Enter audit information about the
active file and click Continue to save the file.
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Print
Print the parameters in your instrument method.
Home Page
View the Home Page window - Roadmap view.
Help
View Help for the Instrument Setup page that is
currently displayed.
Thermo Fisher Scientific
Instrument Setup
Instrument Setup Window
Exactive Instrument Setup - New Method Page
Use the New Method page to specify the type of mass spectrometer
experiment you plan to perform. See Figure 3-4.
Figure 3-4.
New Method page of Exactive Instrument Setup window
The types of experiment you can specify in the New Method page are as
follows:
Parameter
Description
select experiment type
General MS or MSn
❖
Displays the MS Detector Setup page. In
addition, the Exactive mass spectrometer
provides default segment settings and scan
event settings for performing a general MS or
MSn experiment.
To display this page
Click Instrument Setup from the Roadmap View of the Home
Page window or choose GoTo > Instrument Setup.
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Instrument Setup
MS Detector Setup Page
MS Detector Setup Page
Use the MS Detector Setup page to set up your mass spectrometer. See
Figure 3-5. Use this page to specify values for the mass spectrometer
parameters and save the settings as an Instrument Method.
Figure 3-5.
MS Detector Setup page
Use the MS Detector Setup page to specify the following settings:
Parameter
Description
Run Settings
Use the Run Settings area (top region of the page) to define the
MS acquisition time, divide the acquisition time into segments, and
specify the start and end time of each segment. The total acquisition
time can be divided into any number of segments up to 50 segments
where the greatest number of segments possible is determined by the
minimum segment time of 0.1 minutes. For example, the maximum
number of segments for a 4 minute acquisition time can be no greater
than 40 segments whereas a 100 minute acquisition time can be
divided into no more than 50 segments.
Note Align segments and acquisition time with the settings for other
instruments. ▲
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Instrument Setup
MS Detector Setup Page
Parameter
Description
Segments
Displays an integer that indicates the number of
scan segments to occur during the period of
time specified in the Acquisition Time spin box.
To change this number, enter the number of
segments in the Segments spin box.
Alternatively, click the arrows in the spin box to
increment [up arrow] or decrement [down
arrow] the value. When you increase the
number, the selected segment is divided into
equally timed segments. When you decrease the
number, the appropriate number of segments to
the right of the selected segment is removed.
The maximum number of segments is 50.
The Segments bar provides a graphic
representation of the scan segments. To specify
the start and stop time of each segment, position
the cursor between adjacent segments and drag
the segments along the Segments bar.
Alternatively, click a segment on the bar and
enter its duration in minutes in the Acquisition
Time spin box.
Acquisition Time
Displays the total mass spectrometer acquisition
time in minutes for a run. The range is from
0.1 minute to 10000 minutes. To specify the
total acquisition time, enter the time in the
Acquisition Time spin box. The Exactive mass
spectrometer rescales the Segments bar to
correspond to the specified time range for the
acquisition time.
Start Delay
Specifies a time delay (in minutes) before the
start of acquisition. The range is from 0 to 5000
minutes. To specify a time delay, enter the time
in the Start Delay text box. Alternatively, click
the arrows in the spin box to increment [up
arrow] or decrement [down arrow] the value.
Note The start delay is added to the total
acquisition time. ▲
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Instrument Setup
MS Detector Setup Page
Parameter
Description
Segments Bar
Use this bar to divide the acquisition time
period into segments (intervals) of time.
Segments can be divided as follows:
•
To divide the total acquisition time
(specified by the Acquisition Time spin box)
into equal segments of time, enter the total
number of segments in the Segments spin
box. The initial allocation of time for each
equal segment is given in the Duration spin
box.
•
To specify the time of a segment, click the
segment on the bar to select it and enter its
duration in the Duration spin box.
•
To divide a segment in half without
changing the total acquisition time, select
the segment. Then use the Segments spin
box to increment the number of segments
by one. The segment will be divided in
halves; further clicks will divide the selected
segment in halves again.
•
Click and drag the
cursor located
between adjacent segments to manually
adjust the segment time.
Segment Settings
Use the Segment Settings area (middle region of the page) to set up
one or more scan events (up to a maximum of 500 scan events) for the
selected segment.
Note When you increase the number of segments, new segments
inherit the settings of the previously selected segment. ▲
Tune file
Displays the current *.mstune file. To change
the tune file, click in the text box and enter a
new file name. Alternatively, click the
button next to the text box and browse for the
new tune file.
Note An invalid tune file setting is indicated by
a pink background. You must fix invalid settings
before you can save the active instrument
method or before you can change scan event
settings. ▲
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Instrument Setup
MS Detector Setup Page
Parameter
Description
Locking
Displays the lock masses used for the current
segment. The field shows Off when no lock
mass collection is used.
Note During a scan, the Exactive mass
spectrometer uses only the lock masses with a
polarity that matches the ion mode. ▲
Click into the field to display the Locking dialog
box of the MS Detector Setup page, where you
can edit the active lock mass collection.
Scan Events
Displays the number of scan events to be
performed during the period of time specified in
the Duration spin box. Each scan event is
represented by a row in the Scan Event table. To
change this number, enter the number of events
in the Scan Events spin box. Alternatively, click
the arrows in the spin box to increment [up
arrow] or decrement [down arrow] the value.
You can specify 1 to 500 scan events for a
segment; the maximum number of scan events
added over all segments is 500.
Duration
Displays the duration in minutes of the active
segment. To specify the duration of each
segment, click a segment on the Segments bar
and enter its duration in minutes in the
Duration spin box. The start time remains the
same and the end time changes to correspond to
the new duration. Alternatively, position the
cursor between adjacent segments and drag
the segments along the Segments bar.
Scan Event
❖
The settings in this table tell the MS detector
what scan settings to use for the selected scan
event. Each table row represents a scan event.
To display this page
1. In the Home Page, click Instrument Setup.
2. In the New Method page, click General MS or MSn.
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3-11
Instrument Setup
MS Detector Setup Page
Scan Event Table
The settings in this table tell the mass spectrometer what scan settings to
use for the selected scan event. Each table row represents a scan event.
The number of scan events is determined by the Scan Events spin box.
See Figure 3-6.
Figure 3-6.
Scan Event table of the MS Detector Setup page
To change the content of a table cell, click into it. Then, either type a
new number into a text field or select one of the presented options.
Note Table cells that show gray values indicate that tune default values
are used. Selecting a tune default value means that any value change in
the tune file will be applied automatically to the active method. This
includes changes after saving the active method file.
If you intend to use a value that will not be changed unless on explicit
demand, consider using that value directly. ▲
Use the Scan Event table to specify the following parameters:
3-12
•
Polarity
•
Microscans
•
Resolution
•
AGC Target
•
Maximum Inject Time
•
Scan Range
•
Fragmentation
•
Ionization
Exactive Software Manual (P/N 1249910, Revision C)
Thermo Fisher Scientific
Instrument Setup
MS Detector Setup Page
Polarity
The Exactive mass spectrometer can detect either positive or negative
polarity ions during a scan, but not both simultaneously. The options
for ion polarity mode are as follows:
•
Tune default
•
Positive
Sets the mass spectrometer to positive ion detection during a scan.
•
Negative
Sets the mass spectrometer to negative ion detection during a scan.
Note Fast Polarity Switching allows analyzing ions of different polarity
in the scan events within a segment. ▲
Microscans
This column shows the number of microscans to be performed in the
currently selected scan event. In addition to the tune default value, you
can select 1, 2, 3, 4, 5, or 10 microscans.
Resolution
Use this table cell to select the mass resolution for FTMS analysis used
during the currently selected scan event. The mass resolution of the
Orbitrap FTMS analyzer is proportional to 1/sqrt(m/z). The options are
as follows:
•
Tune default,
•
Medium (10000 @ 10 Hz).
•
Enhanced (25000 @ 4 Hz),
•
High (50000 @ 2 Hz),
•
Ultra high (100000 @ 1 Hz)
Note The scan time increases with increasing resolution and detect time.
At a resolution setting of 100000, the scan speed is about 1 scan/sec. At
a resolution setting of 10000, the scan speed is about 10 scans/sec. ▲
AGC Target
This column shows the AGC target value for the currently selected scan
event. The AGC target value controls the number of ions that are
injected into the Orbitrap mass analyzer. The options are as follows:
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3-13
Instrument Setup
MS Detector Setup Page
•
Tune default,
•
Ultimate mass accuracy (5e5),
•
Balanced (1e6),
•
High dynamic range (3e6).
Maximum Inject Time
This column shows the maximum injection time for AGC for the
currently selected scan event. In addition to the tune default value, you
can select 10, 20, 50, 100, 250, 500, or 1000 milliseconds.
Scan Range
This column shows the first mass and last mass of the scan range for the
currently selected scan event. To change the scan range, click into the
table cell to display the Scan range dialog box. See Figure 3-7.
Figure 3-7.
Scan range dialog box of the MS Detector Setup page
Use the Scan Range dialog box to set either minimum and maximum or
center and width of the scan range. If you change one pair of values, the
other pair is changed accordingly.
Note The ratio for maximum-to-minimum cannot exceed 20. If
necessary, Exactive Tune will correct the settings automatically. ▲
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Instrument Setup
MS Detector Setup Page
The Scan range dialog box has the following parameters:
Parameter
Description
Minimum
Use this spin box to select the minimum value for the
scan range (in mass-to-charge ratio units) used during
the currently selected scan event.
To change the value, click the arrows in the spin box
to increment [up arrow] or decrement [down arrow]
the value. You can enter any value from 50.0 to
3999.9. The default value is 120. Alternatively, you
can use the slider.
Maximum
Use this spin box to select the maximum value for the
scan range (in mass-to-charge ratio units) used during
the currently selected scan event.
To change the value, click the arrows in the spin box
to increment [up arrow] or decrement [down arrow]
the value. You can enter any value from 50.1 to
4000.0. The default value is 2000. Alternatively, you
can use the slider.
Center
Use this spin box to select the center mass (in
mass-to-charge ratio units) of the scan range.
To change the value, click the arrows in the spin box
to increment [up arrow] or decrement [down arrow]
the value. You can enter any value from 50.1 to
4000.0. The default value is 1060. Alternatively, you
can use the slider.
Width
Use this spin box to select the width of the scan range
(in mass-to-charge ratio units) used during the
currently selected scan event.
To change the value, click the arrows in the spin box
to increment [up arrow] or decrement [down arrow]
the value. You can enter any value from 0.1 to 3985.0.
The default value is 1880.0. Alternatively, you can use
the slider.
Buttons
(Tune default) Resets the scan range to its default values.
Thermo Fisher Scientific
OK
Saves your changes and closes the dialog box. The new
settings are displayed in the Scan Range column.
Cancel
Discards your changes and closes the dialog box.
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3-15
Instrument Setup
MS Detector Setup Page
Fragmentation
This column is available only when the respective features are installed.
It shows the fragmentation settings for the currently selected scan event.
To change the settings, click into the table cell to display the
Fragmentation dialog box. See Figure 3-8.
Figure 3-8.
Fragmentation dialog box of the MS Detector Setup page
Use the Fragmentation dialog box to activate a fragmentation with the
in-source CID or the HCD collision cell. You can specify the
fragmentation voltages to be used.
The Fragmentation dialog box has the following parameters:
Parameter
Description
In-source CID
Activates the in-source CID.
To change the CID collision energy, click the
arrows in the spin box to increment [up arrow] or
decrement [down arrow] the value. You can set the
CID collision energy to any value from 0.1 to
100 eV.
HCD
Activates the HCD collision cell.
To change the HCD collision energy, click the
arrows in the spin box to increment [up arrow] or
decrement [down arrow] the value. You can set the
HCD collision energy to any value from 10 to
200 eV.
Note This option is available only when HCD gas
is switched on in the active tune file. Otherwise, the
instrument behaves as if no HCD collision cell is
present. ▲
Buttons
3-16
(Tune default)
Resets the collision energy to its default values.
OK
Saves all changes and closes the dialog box. The
new settings are displayed in the Fragmentation
column.
Cancel
Discards all changes and closes the dialog box.
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Thermo Fisher Scientific
Instrument Setup
MS Detector Setup Page
Ionization
This column is available only when an APPI source is configured in the
active tune file. Use the list box to turn on and off the APPI source lamp
when configured with the APCI source.
The options for Ionization are as follows:
•
•
•
•
Tune default
APCI
Select this option to use APCI without photoionization.
APPI
Select this option to use photoionization alone.
APCI + APPI
Select this option to use APPI in combination with APCI.
Locking Dialog Box of the MS Detector Setup Page
Use the Locking dialog box to edit lock mass collections to be used for
the active segment. See Figure 3-9.
Figure 3-9.
Locking Dialog Box of the MS Detector Setup page
The Locking dialog box has the following parameters:
Parameter
Description
Lock mass lists
Lock mass lists
Use the list box to select an existing lock mass
collection.
Displays the New Lock Mass Collection dialog
box where you can enter the name for a a new lock
mass collection.
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3-17
Instrument Setup
MS Detector Setup Page
Parameter
Description
Deletes the active lock mass collection. The lock
masses themselves are still available.
This button is not available when no lock mass
collection is selected.
Displays the Name Change dialog box where you
can edit the name of the active lock mass
collection.
This button is not available when no lock mass
collection is selected.
Available lock masses
The table displays the properties of the available lock masses and
whether they are used in the selected lock mass collection. To change
the sort order, click the respective table column header. To invert the
sort order, click again.
Lock mass table
•
•
Use
Select the check box to use the lock mass. The
lock mass is displayed in the Locking field of
the MS Detector Setup page.
Polarity
Click the symbol to change the polarity of the
lock mass.
Note During a scan, the Exactive mass
spectrometer uses only the lock masses with a
polarity that matches the ion mode. ▲
•
•
m/z
Enter the mass of the lock mass into the field
(with a maximum of five decimals).
Comment
Enter a comment for the lock mass into the
field. This field is optional.
Creates a new lock mass.
Deletes the selected lock masses.
Buttons
3-18
(Tune default)
Uses the lock mass collection stored in the tune
file.
OK
Saves all changes and closes the dialog box.
Cancel
Discards all changes and closes the dialog box.
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Thermo Fisher Scientific
Instrument Setup
MS Detector Setup Page
Parameter
Description
Help
Displays the Help for this dialog box.
Shortcut Menu of the Locking dialog box
The Locking dialog box has a shortcut menu that is displayed when you
right-click into the dialog box.
It has the following commands:
Command
Description
Select all masses in use
Selects all used masses in the active lock
mass collection.
This command is not available when no
lock mass is used.
Import > Merge with
clipboard
Appends the content of the clipboard to
the available lock masses.
Note The clipboard stores lock mass data
as tabulator-separated text files. When
the data in the clipboard are not in this
format, the command is not available. ▲
Import > Replace by
clipboard
Replaces the available lock masses by the
content of the clipboard.
Note The clipboard stores lock mass data
as tabulator-separated text files. When
the data in the clipboard are not in this
format, the command is not available. ▲
Import > Merge with file
content
Opens a dialog box so that you can select
a .csv, .txt, or .xml file that contains a list
of lock masses. The content of the file is
appended to the available lock masses.
See “Exporting and Importing Lock
Masses” on page 5-3 for information
about the format of lock mass files.
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3-19
Instrument Setup
MS Detector Setup Page
Command
Description
Import > Replace by file
content
Opens a dialog box so that you can select
a .csv, .txt, or .xml file that contains a list
of lock masses. All available lock masses
are replaced by the masses contained in
the imported file. The present lock
masses are removed from all existing lock
mass lists. You have to confirm your
action in the Lock mass replacement
dialog box.
See “Exporting and Importing Lock
Masses” on page 5-3 for information
about the format of lock mass files.
Export > Copy selected to
clipboard
Copies the data of the selected lock mass
to the clipboard.
Export > Copy all to
clipboard
Copies the data of all available lock
masses to the clipboard.
Export > Copy selected to
file
Opens the dialog box, where you can
save the data of the selected lock mass(es)
as a .csv, .txt, or .xml file.
See “Exporting and Importing Lock
Masses” on page 5-3 for information
about the format of lock mass files.
Export > Copy all to file
Opens the dialog box, where you can
save the data of all available lock masses
as a .csv, .txt, or .xml file.
See “Exporting and Importing Lock
Masses” on page 5-3 for information
about the format of lock mass files.
❖
To display this dialog box
On the MS Detector Setup page, click into the Locking field of the
Segment settings area.
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Thermo Fisher Scientific
Instrument Setup
Syringe Pump Page
Syringe Pump Page
Use the settings on this page to specify the syringe type and flow rate of
the syringe pump. See Figure 3-10. To activate the settings on the page,
select the Use Syringe Pump check box.
Figure 3-10. Syringe Pump page
The Syringe Pump page has the following parameters:
Parameter
Description
Use Syringe Pump
Select this check box to use the syringe pump
during an acquisition. Use the settings in the
Syringe Pump Settings area to specify the
behavior of syringe pump during the
acquisition.
Syringe Pump Settings
Use the settings in this area to specify the syringe type and flow rate of
the syringe pump. Select the Use Syringe Pump check box to activate
the settings in the area.
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3-21
Instrument Setup
Syringe Pump Page
Parameter
Description
Switch events
Use this spin box to enter the number of switch
positions that are to occur during a run. The
valid range of positions is 1 through 100.
Entering “1” results in the switch remaining
either On or Off throughout the run. Enter a
number between “2” and “100” to change the
state from Off to On or On to Off at multiple
specified times during a run.
The number of positions on the Retention
Time bar corresponds to the number of switch
positions you specify using this spin box.
Start in On state
Use this check box to specify whether the initial
state of the switch at the start of a run is On or
Off.
Stop syringe pump
at end of run
Use this check box to have the Exactive mass
spectrometer turn the syringe pump off when
the run is completed. To turn the syringe pump
off, select this check box. To not have the mass
spectrometer turn the syringe pump off after the
run, ensure that this check box is cleared.
Retention Time bar Use this bar to divide the acquisition time of the
displayed chromatogram into 1 through
100 switch event time durations. To divide the
total acquisition time into equal segments of
time, enter the total number of switch events in
the Switch events spin box. The initial
allocation of time for each equal position
duration is given in the Duration spin box and
the Retention Time bar is divided into the
specified number of switch events. To specify
the time of each switch event duration, click
each position on the bar and enter its duration
in the Duration spin box. Alternatively, click
and drag the
cursor located between
adjacent positions. The Exactive mass
spectrometer displays the duration of the active
switch event in the Duration spin box.
Switch event settings
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Thermo Fisher Scientific
Instrument Setup
Syringe Pump Page
Parameter
Description
Duration
Displays the duration in minutes for the active
switch event on the Retention Time bar. To
change the active switch event, click a different
number on the bar. To change the switch event
duration, enter a new duration in the spin box.
Alternatively, click and drag the
cursor
located between adjacent positions. The
Exactive mass spectrometer displays the updated
duration of the active switch event in the
Duration spin box.
Total starting time
Displays the start time of the active switch
event. The displayed time is the sum of all
switch events that precede the active switch
event plus the start delay.
Syringe type
Use this area to specify the syringe type (Hamilton, Unimetrics, or
Other) and volume. If you select Other, you must specify the inside
diameter of the syringe in the Syringe inner diameter text box.
Thermo Fisher Scientific
Hamilton
Select this option button if you are using a
Hamilton syringe. If you select this option, you
must also specify the syringe volume in the
Volume list box.
Unimetrics
Select this option button if you are using a
Unimetrics syringe. If you select this option,
you must also specify the syringe volume in the
Volume list box.
Other
Select this option button if you are using a
syringe other than a Hamilton or Unimetrics
syringe. If you select this option, you must
specify the inside diameter of the syringe in the
Syringe inner diameter text box.
Volume
Use this list box to specify the syringe volume
for Hamilton and Unimetrics syringes. The
acceptable values depend on the syringe type:
• Hamilton:
0.5, 1, 2, 5, 10, 25, 50, 100, 250, and
500 μL.
• Unimetrics:
10, 25, 50, 100, 250, 500, 1000, 2500,
5000, 10000, 25000, and 50000 μL.
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3-23
Instrument Setup
Syringe Pump Page
Parameter
Description
Syringe inner
diameter
Use this spin box to specify the inside diameter
for syringes other than Hamilton and
Unimetrics syringes. The acceptable range of
values is 0.1 to 35 mm.
To change this value, click the arrows in the spin
box to increment [up arrow] or decrement
[down arrow] the value. Alternatively, enter a
value in the spin box text field.
Flow
Flow Rate
Use this spin box to set the volume of solvent
solution passing through the syringe pump per
unit time. The acceptable range of values
depends on the selected syringe diameter.
To change this value, click the arrows in the spin
box to increment [up arrow] or decrement
[down arrow] the value. Alternatively, enter a
value in the spin box text field.
Buttons
Help
❖
Displays the Help for this page.
To display this page
In the Instrument Setup window, click the Syringe Pump tab.
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Thermo Fisher Scientific
Instrument Setup
Divert Valves Page
Divert Valves Page
Use the Divert Valves page to switch the (optional) switching valves
during a run. See Figure 3-11. The normal LC flow through the
switching valve (Position 1) is to the mass spectrometer. When the
switching valve is activated (Position 2), LC flow is diverted to waste. To
activate the settings on the page, select the Use divert valve check boxes.
Figure 3-11. Divert Valves page
The Divert Valves page has the following parameters:
Parameter
Description
Use divert valve
Use this check box to activate the switching valve
at selected times during a run. To use the
switching valve during a run, select the Use
divert valve check box. The Switch events spin
box and the Start in position 2 check box
become active.
Divert valve settings
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3-25
Instrument Setup
Divert Valves Page
Parameter
Description
Switch events
Use this spin box to select the number of switch
positions that are to occur during a run. The
valid range of positions is 1 through 100.
Selecting “1” results in the switch remaining
either On or Off throughout the run. Select a
number between “2” and “100” to change the
state from Off to On or On to Off at multiple
specified times during a run.
The number of positions on the Retention Time
bar corresponds to the number of switch
positions you specify using this spin box.
Start in position 2
Use this check box to specify that the initial
position of the switch at the start of a run is 2.
Retention Time bar Use this bar to divide the retention time into 1
through 100 intervals of time. You can then
specify the position of the divert valve for each
interval of time. To divide the retention time
into equal segments of time, enter the total
number of segments in the Switch events box.
To specify the time of each segment, click each
segment on the bar and type its duration in the
Duration box.
You can also drag the
adjacent segments.
cursor located between
Switch event settings
Duration
Displays the duration in minutes for the active
switch event on the Retention Time bar. To
change the active switch event, click a different
segment on the bar. To change the switch event
duration, enter a new duration in the spin box.
The duration of each switch event can be set to
any value from 0.01 minutes to the length of the
run. If there is only one switch event, the
Duration spin box is unavailable.
Alternatively, click and drag the
cursor
located between adjacent positions. The Exactive
mass spectrometer displays the updated duration
of the active switch event in the Duration spin
box.
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Thermo Fisher Scientific
Instrument Setup
Divert Valves Page
Parameter
Description
Total starting time
Displays the start time of the active switch event.
The displayed time is the sum of all switch
events that precede the active switch event plus
the start delay.
Buttons
Help
❖
Displays the Help for this page.
To display this page
In the Instrument Setup page, click the Divert Valves tab.
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3-27
Instrument Setup
Contact Closure Page
Contact Closure Page
Use the Contact Closure page to set contact closure settings. See
Figure 3-12. Select the Provide contact closure check box to activate the
controls on this page.
Figure 3-12. Contact Closure page
Use the Contact Closure page to set the following contact closure
settings:
Parameter
Description
Provide contact closure
Use this check box to enable or disable the
controls in the Contact Closure area.
These controls must be enabled in order to
include a timed contact closure program in
an Experiment Method.
Contact closure settings
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Thermo Fisher Scientific
Instrument Setup
Contact Closure Page
Parameter
Description
Switch events
Use this spin box to select the number of
switch positions that are to occur during a
run. The valid range of positions is 1
through 100. Selecting “1” results in the
switch remaining either On or Off
throughout the run. Select a number
between “2” and “100” to change the state
from Off to On or On to Off at multiple
specified times during a run.
The number of positions on the Retention
Time bar corresponds to the number of
switch positions you specify using this spin
box.
Start in Open state
Use this check box to specify whether the
initial state of the contact at the start of a
run is Open or Closed.
Retention Time bar
Use this bar to divide the acquisition time
of the displayed chromatogram into 1
through 100 contact closure position time
durations. To divide the total acquisition
time into equal segments of time, input the
total number of contact closure positions
in the Switch events spin box. The initial
allocation of time for each equal position
duration is given in the Duration spin box
and the Retention Time bar is divided into
the specified number of Position periods.
To specify the time of each position
duration, click each position on the bar
and input its duration in the Duration spin
box.
Alternatively, drag the
cursor located
between adjacent segments.
Switch event settings
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3-29
Instrument Setup
Contact Closure Page
Parameter
Description
Duration
Displays the duration in minutes for the
active switch event on the Retention Time
bar. To change the active switch event,
click a different number on the bar. To
change the switch event duration, enter a
new duration in the spin box.
The duration of each position can be set to
any value from 0.01 minutes to the length
of the run. If there is only one switch
event, the Duration box is unavailable.
Alternatively, click and drag the
cursor
located between adjacent positions. The
Exactive mass spectrometer displays the
updated duration of the active switch event
in the Duration spin box.
Total starting time
Displays the start time of the active switch
event. The displayed time is the sum of all
switch events that precede the active switch
event plus the start delay.
Buttons
Help
❖
Displays the Help for this page.
To display this page
In the Instrument Setup page, click the Contact Closure tab.
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Instrument Setup
Summary Page
Summary Page
The Method Summary page displays the parameters for MS detector
setup, syringe pump, divert valves, and contact closure that you specified
in the other pages. See Figure 3-13.
Figure 3-13. Summary page
Note The content of this page will be printed together with the
information for other instruments. ▲
❖
To display this page
In the Instrument Setup view, click the Summary tab.
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Instrument Setup
Summary Page
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Chapter 4
Explore Exactive Tune
This chapter provides information about Exactive Tune, its views,
functions, and features.
Contents
Thermo Fisher Scientific
•
Exactive Tune Overview
•
Exactive Tune Menus
•
Toolbar
•
Tasks Panel
•
Display Panel
•
Dialog Boxes
Exactive Software Manual (P/N 1249910, Revision C)
4-1
Explore Exactive Tune
Exactive Tune Overview
Exactive Tune Overview
The Exactive Tune program is used to operate the Exactive mass
spectrometer. Figure 4-14 shows Exactive Tune. To access information
about Exactive Tune, use the title bar, the toolbar, menu commands,
display views, and Help.
Menu Bar
Toolbar
Display Panel
Tasks Panel
Figure 4-14. Exactive Tune
❖
To display this window
•
Choose Start > Programs > Thermo Exactive > ExactiveTune, or
•
Click
on the desktop.
Note When you are running Exactive Tune, an Exactive Tune icon ( )
is displayed in the Microsoft® Windows® system tray. Double-click the
icon to display the Exactive Tune window when it is minimized.
Right-click the icon to display a shortcut menu that provides
commands for restoring or terminating Exactive Tune. ▲
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Explore Exactive Tune
Exactive Tune Overview
Title Bar
The Exactive Tune title bar displays the name of the program, the name
of the current Tune Method, and the instrument status. An asterisk
indicates a Tune Method with unsaved changes.
Menus
The Exactive Tune menus are as follows:
•
File Menu
•
Windows Menu
•
Help Menu
Toolbar
The Toolbar provides symbol shortcuts for frequently used commands.
It is located below the title bar of the Exactive Tune window.
Tasks Panel
The tasks panel on the left side of the Exactive Tune window comprises
five windows:
•
The Instrument Control Window on the left side of the Exactive
Tune window comprises three windows:
− Scan Parameters Window for defining a scan depending on the
scan mode and scan type combination.
− API Source window for displaying and editing parameters of the
API source. The window adapts name and parameters of the
currently detected source. At present, Exactive Tune provides the
following API source windows:
ESI Source Window
HESI Source Window
NSI Source Window
APCI Source Window
APPI Source Window
− Acquisition Window for acquiring and storing measurement
data.
•
Thermo Fisher Scientific
Tune Window for optimizing the tune of the mass spectrometer.
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Exactive Tune Overview
•
Calibrate Window for performing an automatic optimization of the
calibration parameters.
•
Evaluate Window for performing an automatic check of the
instrument precision.
•
Vacuum / Bakeout Window for displaying the pressure values at the
vacuum gauges and performing an instrument bakeout.
Display Panel
The display panel on the right side of the Exactive Tune window
comprises up to five windows:
4-4
•
Spectrum Window for displaying a real-time data plot. The
spectrum window is always visible.
•
Instrument Status Window for displaying instrument parameters.
•
Messages Window for displaying current status information about
the instrument, the control service, or other programs.
•
Analysis Graphs Window for displaying a real-time graph.
•
Debug Messages Window for displaying messages that can be used
during software development. The debug messages window is not
available for standard users.
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Exactive Tune Menus
Exactive Tune Menus
The Exactive Tune window has the following menus:
•
File Menu
•
Windows Menu
•
Reports Menu
•
Help Menu
File Menu
The File menu provides commands for file and program operations. It
has the following commands:
Command
Description
Load Tune File
Displays a dialog box where you can find and open
a tune file (*.mstune) that already exists.
Save Tune File
Saves the active tune file with the current settings.
Note Do not overwrite the default tune file
C:\Xcalibur\methods\ESI_Installation.mstune! ▲
Save Tune File as Opens a dialog box where you can enter a new file
name and select the location (disk and directory)
where you want to save it. Click Save to save the
tune file with the current settings.
Note Do not overwrite the default tune file
C:\Xcalibur\methods\ESI_Installation.mstune! ▲
Terminate
Closes the active window. If the active tune file
contains unsaved changes, a dialog box warns about
losing data when you terminate the program.
Windows Menu
The Windows menu provides commands for customizing the
information displayed in the Exactive Tune window. It has the following
commands:
Thermo Fisher Scientific
Command
Description
View > Show all
Displays all windows of Exactive Tune.
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Exactive Tune Menus
Command
Description
Spectrum
Displays the Spectrum Window.
The Spectrum Window is always visible.
Instrument Status
Displays/Hides the Instrument Status
Window.
The system highlights the icon to the left of
the command if the window is active.
Deselect the command to hide the window.
Messages
Displays/Hides the Messages Window.
The system highlights the icon to the left of
the command if the window is active.
Deselect the command to hide the window.
Analysis Graphs
Displays/Hides the Analysis Graphs
Window.
The system highlights the icon to the left of
the command if the window is active.
Deselect the command to hide the window.
Debug Messages
Displays/Hides the Debug Messages
Window.
The system highlights the icon to the left of
the command if the window is active.
Deselect the command to hide the window.
Note The debug messages window is not
available for standard users. ▲
Note Exactive Tune may open some windows (the analysis graphs
window, for example) without user interaction if new important
information is available. ▲
Reports Menu
The Reports menu groups commands that provide information about
calibration reports. It has the following commands:
4-6
Command
Description
Spectral Mass Calibration
(neg) > Latest
Opens the latest negative mode
calibration report in PDF format.
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Exactive Tune Menus
Command
Description
Spectral Mass Calibration
(neg) > Last
Displays the list of up to five (5) negative
mode calibration reports.
To open a report, double-click any of the
spectral mass calibrations from the list.
Spectral Mass Calibration
(pos) > Latest
Opens the latest positive mode
calibration report in PDF format.
Spectral Mass Calibration
(pos) > Last
Displays the list of up to five (5) positive
mode calibration reports.
To open a report, double-click any of the
spectral mass calibrations from the list.
All Reports
Opens a new window with a list of all
previously acquired spectral mass
calibrations.
Help Menu
The Help menu groups commands that provide information about
Exactive Tune. It has the following commands:
Thermo Fisher Scientific
Command
Description
Help Overview
Displays Exactive Tune Help.
Help Content
Displays the table of contents for Exactive Tune
Help.
Help Index
Displays the index for Exactive Tune Help.
About
Displays the About dialog box with information
about the instrument and the current Exactive Tune
version.
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Toolbar
Toolbar
The Exactive Tune toolbar provides symbol shortcuts for frequently
used commands. It is located below the title bar of the Exactive Tune
window. To activate a toolbar function, click the corresponding toolbar
button.
Some symbols provide information about the current statuses of
respective instrument components either by their color or by displaying
a tooltip when you move the mouse pointer over them.
The following functions are available:
Button
Description
General instrument state
On / Standby / Off
Run by Xcalibur
Click to toggle between mass spectrometer On, mass
spectrometer Standby, and mass spectrometer Off. The button
reflects the instrument status:
• When the mass spectrometer is On, Exactive Tune displays
•
.
When the mass spectrometer is in Standby, Exactive Tune
displays
•
.
When the mass spectrometer is Off, Exactive Tune displays
.
The status of this button controls also the statuses of gas flow and
syringe pump use (if present).
If the Exactive mass spectrometer is controlled by an Xcalibur
sequence, Exactive Tune displays
. The acquisition can only
be stopped from Xcalibur Sequence Setup View.
Open
Displays a dialog box where you can find and open a *.mstune
file that already exists. Alternatively, choose File > Load Tune
File.
Save
Opens a dialog box where you can select the location (disk and
directory) where you want to save the tune file. Alternatively,
choose File > Save Tune File as.
This button is not available when the settings of the active tune
file are not changed.
4-8
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Toolbar
Button
Description
Divert Valve A
Position 1 or Position 2
Divert Valve B
Position 1 or Position 2
Click to switch the valve position directly. The button reflects the
valve status (connected positions, Valve “a”).
Click to switch the valve position directly. The button reflects the
valve status (connected positions, Valve “b”).
Syringe Pump Settings
Click to switch on/off the syringe pump (if present). A symbol in
the lower right corner of the button indicates the current status of
Syringe Pump On or Syringe the syringe pump:
Pump Off
• When the syringe pump is On, Exactive Tune displays
.
•
When the syringe pump is Off, Exactive Tune displays
.
•
When the syringe pump is in an unknown state, Exactive
Tune displays
.
Click the down arrow to display the Syringe Pump Settings
dialog box. Use the dialog box to specify syringe pump
parameters or to manually operate the syringe pump.
Communication Status
Shows the actual communication status of the system:
• Green: communication with instrument is ok.
• Yellow: only service is accessible (no instrument).
• Red: communication is broken (no instrument, no service).
Hardware Status
Shows the actual hardware status of the system (top instrument
tree state):
• Green: all readbacks are in specifications (green hooks).
• Red: one or more readbacks are out of range.
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Toolbar
Button
Description
Performance Status
Shows the actual performance status of the system:
• Green: the last evaluation/calibration was successful.
• Yellow: the last evaluation/calibration was successful, but is
out of date.
• Red: the evaluation/calibration was not successful.
By default, the performance status icon turns yellow 25 hours
after the last successful mass calibration or check. With exception
of standard users, users can change this value in the System node
of the instrument status window according to their mass
accurracy requirements.
4-10
Procedure active
If a procedure is active (for example, system bakeout or tune)
Exactive Tune displays an animated icon next to the performance
status button.
Acquisition indicator
If the Exactive mass spectrometer is acquiring data, Exactive Tune
displays an animated icon next to the performance status button.
Exactive Software Manual (P/N 1249910, Revision C)
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Tasks Panel
Tasks Panel
Use the windows of the tasks panel to perform procedures that maintain
the quality of measurements with the Exactive mass spectrometer.
The tasks panel is always visible. The windows in the tasks panel can be
minimized or maximized. Click the title bar of an individual window to
display it.
•
Instrument Control Window
•
Tune Window
•
Calibrate Window
•
Evaluate Window
•
Vacuum / Bakeout Window
Instrument Control Window
Use the windows of the Instrument Control window to set individual
physical settings and to acquire scans. The following windows are
available:
•
Scan Parameters Window
•
API Source Window (one of the following)
− ESI Source Window
− HESI Source Window
− NSI Source Window
− APCI Source Window
− APPI Source Window
•
Acquisition Window
The Instrument Control window is always visible. Click the title bar of
an individual window to display it. Click again to hide it. To change the
order of windows within the Instrument Control window, drag
individual windows by their title bars to the new places.
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Tasks Panel
Scan Parameters Window
Use the Scan Parameters window to define a scan depending on the
selected scan mode and scan type combination. See Figure 4-15.The
Exactive mass spectrometer updates the scan parameters only after you
click Apply or select the Hot link check box.
Figure 4-15. Scan Parameters window
The parameters available in the Scan Parameters window are as follows:
Parameter
Description
History
Click to display the Scan Parameters
History dialog box. Here, select from a list
of recent scans based upon short scan
descriptions. The maximum number of list
items is 100.
After a change of parameters, the history is
updated when you click Apply or when you
change the status of the Hot link check box.
Scan Range
4-12
Exactive Software Manual (P/N 1249910, Revision C)
Displays the current scan range. To change
the settings, click into the field to display
the Scan Range dialog box.
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Tasks Panel
Parameter
Description
Fragmentation
Displays the current settings for
HCD fragmentation and in-source
CID fragmentation. If no fragmentation
type is selected, the text field shows None.
(Instruments equipped with an
HCD collision cell show either HCD Gas
Off or HCD Gas On.) To change the
settings, click into the field to display the
Fragmentation dialog box.
This parameter is available only when the
respective features are installed.
Note Automatic tuning is disabled when
in-source CID fragmentation is on. ▲
Resolution
Use this list box to select the mass resolution
for FTMS analysis. The mass resolution of
the Orbitrap analyzer is proportional to
1/sqrt(m/z). The options are as follows:
• Medium (10000 @ 10 Hz).
• Enhanced (25000 @ 4 Hz),
• High (50000 @ 2 Hz),
• Ultra high (100000 @ 1 Hz)
Note The scan time increases with
increasing resolution and detect time. At a
resolution setting of 100000, the scan speed
is about 1 scan/sec. At a resolution setting of
10000, the scan speed is about
10 scans/sec. ▲
Thermo Fisher Scientific
Polarity
Use this list to toggle between positive ion
and negative ion polarity.
Microscans
Use the list box to select the number of
microscans to be performed. Available
options are 1, 2, 3, 4, 5, or 10 microscans.
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Tasks Panel
Parameter
Description
Lock masses
Displays the active lock masses. During a
scan, the Exactive mass spectrometer uses
only the lock masses with a polarity that
matches the ion mode. If no lock masses are
selected, the text field shows Off. To change
the settings, click into the field to display
the Lock Masses dialog box.
Note Exactive Tune allows using active lock
masses in user-defined calibration mass
lists. ▲
AGC target
Use the list box to select the AGC target
value. The AGC target value controls the
number of ions that are injected into the
Orbitrap mass analyzer. The options are as
follows:
• Ultimate mass accuracy (5e5),
• Balanced (1e6),
• High dynamic range (3e6).
Maximum inject time
Use the list box to select maximum injection
time for AGC. Available options are 10, 20,
50, 100, 250, 500, or 1000 milliseconds.
Buttons
Apply
Sends all changes to the instrument.
Help
Displays the Help for this window.
Hot Link
Select the Hot link check box to allow
Exactive Tune to send any changes
immediately to the instrument. A green
frame around the parameter box indicates
an active hot link.
❖
To display this window
Click the Scan Parameters window title bar in the Instrument
Control window.
4-14
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Tasks Panel
ESI Source Window
Use the ESI source window to specify electrospray ionization (ESI)
source parameters. See Figure 4-16. The Exactive mass spectrometer
updates the ESI source parameters only after you click Apply or with
the Hot link check box being selected.
Figure 4-16. ESI source window
Note This window is available only when the Exactive mass
spectrometer has detected an installed ESI source. ▲
The ESI source window has the following parameters:
Parameter
Description
Sheath Gas Flow Rate
Displays the setpoint ESI source sheath gas
flow rate (in arbitrary units). To change the
setpoint flow rate, click the arrows in the
Sheath Gas Flow Rate spin box to increment
[up arrow] or decrement [down arrow] the
value. You can set the sheath gas flow rate to
any value from 0 to 80 units. Alternatively,
you can enter a value in the spin box text
field. The mass spectrometer changes the
flow rate when you click Apply or with the
Hot link check box being selected.
The Sheath Gas Flow Rate readback is to the
right of the spin box. This readback displays
the actual flow rate (in arbitrary units).
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Tasks Panel
Parameter
Description
Aux Gas Flow Rate
Displays the setpoint ESI source auxiliary gas
flow rate (in arbitrary units). To change the
setpoint flow rate, click the arrows in the Aux
Gas Flow Rate spin box to increment [up
arrow] or decrement [down arrow] the value.
You can set the flow rate to any value from 0
to 40 units. Alternatively, you can enter a
value in the spin box text field. The mass
spectrometer changes the flow rate when you
click Apply or with the Hot link check box
being selected.
The Aux Gas Flow Rate readback is to the
right of the spin box. This readback displays
the actual flow rate (in arbitrary units).
Sweep Gas Flow Rate
Displays the setpoint ESI source sweep gas
flow rate. To change the setpoint flow rate,
click the arrows in the Sweep Gas Flow Rate
spin box to increment [up arrow] or
decrement [down arrow] the value. You can
set the flow rate to any value from 0 to
10 units. Alternatively, you can enter a value
in the spin box text field. The mass
spectrometer changes the flow rate when you
click Apply or with the Hot link check box
being selected.
The Sweep Gas Flow Rate readback is to the
right of the spin box. This readback displays
the actual flow rate (in arbitrary units).
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Tasks Panel
Parameter
Description
Spray Voltage
Displays the setpoint ESI source spray
voltage (absolute value, in kilovolts). To
change the setpoint spray voltage, click the
arrows in the Spray Voltage spin box to
increment [up arrow] or decrement [down
arrow] the value. You can set the spray
voltage to any value from 0.0 to 8.0 kV. The
sign of the spray voltages changes
automatically with the ion polarity mode:
positive for positive ions and negative for
negative ions. Alternatively, you can enter a
value in the spin box text field. The mass
spectrometer changes the spray voltage when
you click Apply or with the Hot link check
box being selected.
The Spray Voltage readback is to the right of
the spin box. This readback displays the
actual spray voltage (absolute value, in
kilovolts).
Spray Current
This readback displays the actual ESI source
spray current (in microamperes). The
ESI spray current is typically less than 5 μA.
Capillary Temperature Displays the setpoint ESI source heated
capillary temperature (in degrees Celsius). To
change the setpoint heated capillary
temperature, click the arrows in the Capillary
Temp spin box to increment [up arrow] or
decrement [down arrow] the value. You can
set the heated capillary temperature to any
value from 0 to 450 °C. Alternatively, you
can enter a value in the spin box text field.
The mass spectrometer changes the heated
capillary temperature when you click Apply
or with the Hot link check box being
selected.
The Capillary Temperature readback is to the
right of the spin box. This readback displays
the actual temperature (in degrees Celsius) of
the heated capillary.
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Tasks Panel
Parameter
Description
Capillary Voltage
Displays the setpoint ESI source heated
capillary voltage (in volts). To change the
setpoint heated capillary voltage, click the
arrows in the Capillary Voltage spin box to
increment [up arrow] or decrement [down
arrow] the value. You can set the heated
capillary voltage to any value from -140 to
+140 V. Alternatively, you can enter a value
in the spin box text field. The mass
spectrometer changes the heated capillary
voltage when you click Apply or with the
Hot link check box being selected. A
Capillary Voltage readback is not displayed.
Tube Lens Voltage
Displays the setpoint ESI source tube lens
voltage (in volts). You can set the tube lens
voltage to any value from -250 to +250 V. To
change the setpoint tube lens voltage, click
the arrows in the Tube Lens Voltage spin box
to increment [up arrow] or decrement [down
arrow] the value. The values you can set the
tube lens voltage to vary with the mass of the
ions being analyzed and the polarity of the
ions. Alternatively, you can enter a value in
the spin box text field. The mass
spectrometer changes the tube lens voltage
when you click Apply or with the Hot link
check box being selected. A Tube Lens
Voltage readback is not displayed.
Skimmer Voltage
Displays the setpoint ESI source skimmer
voltage (in volts). You can set the skimmer
voltage to any value from -50 to +50 V. To
change the setpoint skimmer voltage, click
the arrows in the Skimmer Voltage spin box
to increment [up arrow] or decrement [down
arrow] the value. Alternatively, you can enter
a value in the spin box text field. The mass
spectrometer changes the skimmer voltage
when you click Apply or with the Hot link
check box being selected. A Skimmer Voltage
readback is not displayed.
Buttons
4-18
Apply
Sends all changes to the instrument.
Help
Displays the Help for this window.
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Tasks Panel
Parameter
Description
Hot Link
Select the Hot link check box to allow
Exactive Tune to send any changes
immediately to the instrument. A green
frame around the parameter box indicates an
active hot link.
❖
To display this window
Click the ESI source window title bar in the Instrument Control
window.
HESI Source Window
Use the HESI source window to specify heated-electrospray ionization
(H-ESI) source parameters. See Figure 4-17. The Exactive mass
spectrometer updates the H-ESI source parameters only after you click
Apply or with the Hot link check box being selected.
Figure 4-17. HESI source window
Note This window is available only when the Exactive mass
spectrometer has detected an installed H-ESI source. The H-ESI source
is the standard API source of the Exactive mass spectrometer. ▲
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Tasks Panel
The HESI source window has the following parameters:
Parameter
Description
Sheath Gas Flow Rate
Displays the setpoint H-ESI source sheath
gas flow rate (in arbitrary units). To change
the setpoint flow rate, click the arrows in the
Sheath Gas Flow Rate spin box to increment
[up arrow] or decrement [down arrow] the
value. You can set the sheath gas flow rate to
any value from 0 to 80 units. Alternatively,
you can enter a value in the spin box text
field. The mass spectrometer changes the
flow rate when you click Apply or with the
Hot link check box being selected.
The Sheath Gas Flow Rate readback is to the
right of the spin box. This readback displays
the actual flow rate (in arbitrary units).
Aux Gas Flow Rate
Displays the setpoint H-ESI source auxiliary
gas flow rate (in arbitrary units). To change
the setpoint flow rate, click the arrows in the
Aux Gas Flow Rate spin box to increment
[up arrow] or decrement [down arrow] the
value. You can set the flow rate to any value
from 0 to 40 units. Alternatively, you can
enter a value in the spin box text field. The
mass spectrometer changes the flow rate
when you click Apply or with the Hot link
check box being selected.
The Aux Gas Flow Rate readback is to the
right of the spin box. This readback displays
the actual flow rate (in arbitrary units).
Sweep Gas Flow Rate
Displays the setpoint H-ESI source sweep gas
flow rate. To change the setpoint flow rate,
click the arrows in the Sweep Gas Flow Rate
spin box to increment [up arrow] or
decrement [down arrow] the value. You can
set the flow rate to any value from 0 to
10 units. Alternatively, you can enter a value
in the spin box text field. The mass
spectrometer changes the flow rate when you
click Apply or with the Hot link check box
being selected.
The Sweep Gas Flow Rate readback is to the
right of the spin box. This readback displays
the actual flow rate (in arbitrary units).
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Tasks Panel
Parameter
Description
Spray Voltage
Displays the setpoint H-ESI source spray
voltage (absolute value, in kilovolts). To
change the setpoint spray voltage, click the
arrows in the Spray Voltage spin box to
increment [up arrow] or decrement [down
arrow] the value. You can set the spray
voltage to any value from 0.0 to 8.0 kV. The
sign of the spray voltages changes
automatically with the ion polarity mode:
positive for positive ions and negative for
negative ions. Alternatively, you can enter a
value in the spin box text field. The mass
spectrometer changes the spray voltage when
you click Apply or with the Hot link check
box being selected.
The Spray Voltage readback is to the right of
the spin box. This readback displays the
actual spray voltage (absolute value, in
kilovolts).
Spray Current
This readback displays the actual
H-ESI source spray current (in
microamperes). The H-ESI spray current is
typically less than 5 μA.
Capillary Temperature Displays the setpoint H-ESI source heated
capillary temperature (in degrees Celsius). To
change the setpoint heated capillary
temperature, click the arrows in the Capillary
Temp spin box to increment [up arrow] or
decrement [down arrow] the value. You can
set the heated capillary temperature to any
value from 0 to 450 °C. Alternatively, you
can enter a value in the spin box text field.
The mass spectrometer changes the heated
capillary temperature when you click Apply
or with the Hot link check box being
selected.
The Capillary Temperature readback is to the
right of the spin box. This readback displays
the actual temperature (in degrees Celsius) of
the heated capillary.
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Tasks Panel
4-22
Parameter
Description
Capillary Voltage
Displays the setpoint H-ESI source heated
capillary voltage (in volts). To change the
setpoint heated capillary voltage, click the
arrows in the Capillary Voltage spin box to
increment [up arrow] or decrement [down
arrow] the value. You can set the heated
capillary voltage to any value from -140 to
+140 V. Alternatively, you can enter a value
in the spin box text field. The mass
spectrometer changes the heated capillary
voltage when you click Apply or with the
Hot link check box being selected. A
Capillary Voltage readback is not displayed.
Tube Lens Voltage
Displays the setpoint H-ESI source tube lens
voltage (in volts). You can set the tube lens
voltage to any value from -250 to +250 V. To
change the setpoint tube lens voltage, click
the arrows in the Tube Lens spin box to
increment [up arrow] or decrement [down
arrow] the value. The values you can set the
tube lens voltage to vary with the mass of the
ions being analyzed and the polarity of the
ions. Alternatively, you can enter a value in
the spin box text field. The mass
spectrometer changes the tube lens voltage
when you click Apply or with the Hot link
check box being selected. A Tube Lens
Voltage readback is not displayed.
Skimmer Voltage
Displays the setpoint H-ESI source skimmer
voltage (in volts). You can set the skimmer
voltage to any value from -50 to +50 V. To
change the setpoint skimmer voltage, click
the arrows in the Skimmer Voltage spin box
to increment [up arrow] or decrement [down
arrow] the value. Alternatively, you can enter
a value in the spin box text field. The mass
spectrometer changes the skimmer voltage
when you click Apply or with the Hot link
check box being selected. A Skimmer Voltage
readback is not displayed.
Exactive Software Manual (P/N 1249910, Revision C)
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Tasks Panel
Parameter
Description
Heater Temperature
Displays the setpoint temperature (in degrees
Celsius) of the H-ESI source heater, which
heats the auxiliary gas. To change the
setpoint vaporizer temperature, click the
arrows in the Heater Temp spin box to
increment [up arrow] or decrement [down
arrow] the value. You can set the vaporizer
temperature to any value from 0 to 600 °C.
Alternatively, you can enter a value in the
spin box text field. The mass spectrometer
changes the vaporizer temperature when you
click Apply or with the Hot link check box
being selected.
The Heater Temperature readback is to the
right of the spin box. This readback displays
the actual temperature (in degrees Celsius) of
the vaporizer.
Buttons
Apply
Sends all changes to the instrument.
Help
Displays the Help for this window.
Hot Link
Select the Hot link check box to allow
Exactive Tune to send any changes
immediately to the instrument. A green
frame around the parameter box indicates an
active hot link.
Initial Heated ESI Settings
Liquid Flow Rate
(μL/min)
Heater Temp
(°C)
Capillary Temp
(°C)
Sheath Gas Flow Rate
(arbitrary units)
Aux Gas Flow Rate
(arbitrary units)
Spray Voltage
(kV)
5
Off–50
240
5
0
+3 positive mode
-2.5 negative mode
200
250–300
350
35
30
+3 positive mode
-2.5 negative mode
500
300–400
380
60
35
+3 positive mode
-2.5 negative mode
1000
350–450
400
75
35
+3 positive mode
-2.5 negative mode
❖
To display this window
Click the HESI source window title bar in the Instrument Control
window.
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NSI Source Window
Use the NSI source window to specify nanospray ionization (NSI)
source parameters. See Figure 4-18. The Exactive mass spectrometer
updates the NSI source parameters only after you click Apply or with
the Hot link check box being selected.
Figure 4-18. NSI source window
Note This window is available only when the Exactive mass
spectrometer has detected an installed NSI source. ▲
The NSI source window has the following parameters:
Parameter
Description
Sheath Gas Flow Rate
Displays the setpoint NSI source sheath gas
flow rate (in arbitrary units). To change the
setpoint flow rate, click the arrows in the
Sheath Gas Flow Rate spin box to increment
[up arrow] or decrement [down arrow] the
value. You can set the sheath gas flow rate to
any value from 0 to 80 units. Alternatively,
you can enter a value in the spin box text
field. The mass spectrometer changes the
flow rate when you click Apply or with the
Hot link check box being selected.
The Sheath Gas Flow Rate readback is to the
right of the spin box. This readback displays
the actual flow rate (in arbitrary units).
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Parameter
Description
Aux Gas Flow Rate
Displays the setpoint NSI source auxiliary
gas flow rate (in arbitrary units). To change
the setpoint flow rate, click the arrows in the
Aux Gas Flow Rate spin box to increment
[up arrow] or decrement [down arrow] the
value. You can set the flow rate to any value
from 0 to 40 units. Alternatively, you can
enter a value in the spin box text field. The
mass spectrometer changes the flow rate
when you click Apply or with the Hot link
check box being selected.
The Aux Gas Flow Rate readback is to the
right of the spin box. This readback displays
the actual flow rate (in arbitrary units).
Sweep Gas Flow Rate
Displays the setpoint NSI source sweep gas
flow rate. To change the setpoint flow rate,
click the arrows in the Sweep Gas Flow Rate
spin box to increment [up arrow] or
decrement [down arrow] the value. You can
set the flow rate to any value from 0 to
10 units. Alternatively, you can enter a value
in the spin box text field. The mass
spectrometer changes the flow rate when you
click Apply or with the Hot link check box
being selected.
The Sweep Gas Flow Rate readback is to the
right of the spin box. This readback displays
the actual flow rate (in arbitrary units).
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Parameter
Description
Spray Voltage
Displays the setpoint NSI source spray
voltage (absolute value, in kilovolts). To
change the setpoint spray voltage, click the
arrows in the Spray Voltage spin box to
increment [up arrow] or decrement [down
arrow] the value. You can set the spray
voltage to any value from 0.0 to 8.0 kV. The
sign of the spray voltages changes
automatically with the ion polarity mode:
positive for positive ions and negative for
negative ions. Alternatively, you can enter a
value in the spin box text field. The mass
spectrometer changes the spray voltage when
you click Apply or with the Hot link check
box being selected.
The Spray Voltage readback is to the right of
the spin box. This readback displays the
actual spray voltage (absolute value, in
kilovolts).
Spray Current
This readback displays the actual NSI source
spray current (in microamperes). NSI spray
current is typically less than 5 μA.
Capillary Temperature Displays the setpoint NSI source heated
capillary temperature (in degrees Celsius). To
change the setpoint heated capillary
temperature, click the arrows in the Capillary
Temp spin box to increment [up arrow] or
decrement [down arrow] the value. You can
set the heated capillary temperature to any
value from 0 to 450 °C. Alternatively, you
can enter a value in the spin box text field.
The mass spectrometer changes the heated
capillary temperature when you click Apply
or with the Hot link check box being
selected.
The Capillary Temperature readback is to the
right of the spin box. This readback displays
the actual temperature (in degrees Celsius) of
the heated capillary.
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Parameter
Description
Capillary Voltage
Displays the setpoint NSI source heated
capillary voltage (in volts). To change the
setpoint heated capillary voltage, click the
arrows in the Capillary Voltage spin box to
increment [up arrow] or decrement [down
arrow] the value. You can set the heated
capillary voltage to any value from -140 to
+140 V. Alternatively, you can enter a value
in the spin box text field. The mass
spectrometer changes the heated capillary
voltage when you click Apply or with the
Hot link check box being selected. A
Capillary Voltage readback is not displayed.
Tube Lens Voltage
Displays the setpoint NSI source tube lens
voltage (in volts). You can set the tube lens
voltage to any value from -250 to +250 V. To
change the setpoint tube lens voltage, click
the arrows in the Tube Lens spin box to
increment [up arrow] or decrement [down
arrow] the value. The values you can set the
tube lens voltage to vary with the mass of the
ions being analyzed and the polarity of the
ions. Alternatively, you can enter a value in
the spin box text field. The mass
spectrometer changes the tube lens voltage
when you click Apply or with the Hot link
check box being selected. A Tube Lens
Voltage readback is not displayed.
Skimmer Voltage
Displays the setpoint NSI source skimmer
voltage (in volts). You can set the skimmer
voltage to any value from -50 to +50 V. To
change the setpoint skimmer voltage, click
the arrows in the Skimmer Voltage spin box
to increment [up arrow] or decrement [down
arrow] the value. Alternatively, you can enter
a value in the spin box text field. The mass
spectrometer changes the skimmer voltage
when you click Apply or with the Hot link
check box being selected. A Skimmer Voltage
readback is not displayed.
Buttons
Thermo Fisher Scientific
Apply
Sends all changes to the instrument.
Help
Displays the Help for this window.
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Parameter
Description
Hot Link
Select the Hot link check box to allow
Exactive Tune to send any changes
immediately to the instrument. A green
frame around the parameter box indicates an
active hot link.
❖
To display this window
Click the NSI source window title bar in the Instrument Control
window.
APCI Source Window
Use the APCI source window to specify atmospheric pressure chemical
ionization (APCI) source parameters. See Figure 4-19.The Exactive
mass spectrometer updates the APCI source parameters only after you
click Apply or with the Hot link check box being selected.
Figure 4-19. APCI source window
Note This window is available only when the Exactive mass
spectrometer has detected an installed APCI source. ▲
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The APCI source window has the following parameters:
Parameter
Description
Sheath Gas Flow Rate
Displays the setpoint APCI source sheath gas
flow rate (in arbitrary units). To change the
setpoint flow rate, click the arrows in the
Sheath Gas Flow Rate spin box to increment
[up arrow] or decrement [down arrow] the
value. You can set the sheath gas flow rate to
any value from 0 to 80 units. Alternatively,
you can enter a value in the spin box text
field. The mass spectrometer changes the
flow rate when you click Apply or with the
Hot link check box being selected.
The Sheath Gas Flow Rate readback is to the
right of the spin box. This readback displays
the actual flow rate (in arbitrary units).
Aux Gas Flow Rate
Displays the setpoint APCI source auxiliary
gas flow rate (in arbitrary units). To change
the setpoint flow rate, click the arrows in the
Aux Gas Flow Rate spin box to increment
[up arrow] or decrement [down arrow] the
value. You can set the flow rate to any value
from 0 to 40 units. Alternatively, you can
enter a value in the spin box text field. The
mass spectrometer changes the flow rate
when you click Apply or with the Hot link
check box being selected.
The Aux Gas Flow Rate readback is to the
right of the spin box. This readback displays
the actual flow rate (in arbitrary units).
Sweep Gas Flow Rate
Displays the setpoint APCI source sweep gas
flow rate. To change the setpoint flow rate,
click the arrows in the Sweep Gas Flow Rate
spin box to increment [up arrow] or
decrement [down arrow] the value. You can
set the flow rate to any value from 0 to
10 units. Alternatively, you can enter a value
in the spin box text field. The mass
spectrometer changes the flow rate when you
click Apply or with the Hot link check box
being selected.
The Sweep Gas Flow Rate readback is to the
right of the spin box. This readback displays
the actual flow rate (in arbitrary units).
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Parameter
Description
Discharge Voltage
Displays the actual APCI source discharge
voltage (absolute value, in kilovolts).
Discharge Current
Displays the setpoint APCI source discharge
current (in microamperes). To change the
setpoint discharge current, click the arrows in
the Discharge Current spin box to increment
[up arrow] or decrement [down arrow] the
value. You can set the discharge current to
any value from 0 to 10 μA. (A typical value is
5 μA.) Alternatively, you can enter a value in
the spin box text field. The mass
spectrometer changes the discharge current
when you click Apply or with the Hot link
check box being selected.
The Discharge Current readback is to the
right of the spin box. This readback displays
the actual discharge current (in
microamperes).
Capillary Temperature Displays the setpoint APCI source heated
capillary temperature (in degrees Celsius). To
change the setpoint heated capillary
temperature, click the arrows in the Capillary
Temp spin box to increment [up arrow] or
decrement [down arrow] the value. You can
set the heated capillary temperature to any
value from 0.00 to 300.00 °C. Alternatively,
you can enter a value in the spin box text
field. The mass spectrometer changes the
heated capillary temperature when you click
Apply or with the Hot link check box being
selected.
The Capillary Temperature readback is to the
right of the spin box. This readback displays
the actual temperature (in degrees Celsius) of
the heated capillary.
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Thermo Fisher Scientific
Parameter
Description
Capillary Voltage
Displays the setpoint APCI source heated
capillary voltage (in volts). To change the
setpoint heated capillary voltage, click the
arrows in the Capillary Voltage spin box to
increment [up arrow] or decrement [down
arrow] the value. You can set the heated
capillary voltage to any value from -135 to
+135 V. Alternatively, you can enter a value
in the spin box text field. The mass
spectrometer changes the heated capillary
voltage when you click Apply or with the
Hot link check box being selected. A
Capillary Voltage readback is not displayed.
Tube Lens Voltage
Displays the setpoint APCI source tube lens
voltage (in volts). To change the setpoint
tube lens voltage, click the arrows in the Tube
Lens spin box to increment [up arrow] or
decrement [down arrow] the value. The
values you can set the tube lens voltage to
vary with the mass of the ions being analyzed
and the polarity of the ions. Alternatively,
you can enter a value in the spin box text
field. The mass spectrometer changes the
tube lens voltage when you click Apply or
with the Hot link check box being selected. A
Tube Lens Voltage readback is not displayed.
Skimmer Voltage
Displays the setpoint APCI source skimmer
voltage (in volts). You can set the skimmer
voltage to any value from -50 to +50 V. To
change the setpoint skimmer voltage, click
the arrows in the Skimmer Voltage spin box
to increment [up arrow] or decrement [down
arrow] the value. Alternatively, you can enter
a value in the spin box text field. The mass
spectrometer changes the skimmer voltage
when you click Apply or with the Hot link
check box being selected. A Skimmer Voltage
readback is not displayed.
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Parameter
Description
Vaporizer Temperature Displays the setpoint APCI source vaporizer
temperature (in degrees Celsius). To change
the setpoint vaporizer temperature, click the
arrows in the Vaporizer Temp. spin box to
increment [up arrow] or decrement [down
arrow] the value. You can set the vaporizer
temperature to any value from 0 to 600 °C.
Alternatively, you can enter a value in the
spin box text field. The mass spectrometer
changes the vaporizer temperature when you
click Apply or with the Hot link check box
being selected.
The Vaporizer Temperature readback is to
the right of the spin box. This readback
displays the actual temperature (in degrees
Celsius) of the vaporizer.
Buttons
Apply
Sends all changes to the instrument.
Help
Displays the Help for this window.
Hot Link
Select the Hot link check box to allow
Exactive Tune to send any changes
immediately to the instrument. A green
frame around the parameter box indicates an
active hot link.
❖
To display this window
Click the APCI source window title bar in the Instrument Control
window.
APPI Source Window
Use the APPI source window to specify atmospheric pressure chemical
ionization (APCI) source parameters and turning on and off the
atmospheric pressure photoionization (APPI) lamp. See
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Figure 4-20.The Exactive mass spectrometer updates the APPI source
parameters only after you click Apply or with the Hot link check box
being selected.
Figure 4-20. APPI source window
Note This window is available only when the Exactive mass
spectrometer has detected an installed APPI source. ▲
The APPI source window has the following parameters:
Parameter
Description
Sheath Gas Flow Rate
Displays the setpoint APPI source sheath gas
flow rate (in arbitrary units). To change the
setpoint flow rate, click the arrows in the
Sheath Gas Flow Rate spin box to increment
[up arrow] or decrement [down arrow] the
value. You can set the sheath gas flow rate to
any value from 0 to 80 units. Alternatively,
you can enter a value in the spin box text
field. The mass spectrometer changes the
flow rate when you click Apply or with the
Hot link check box being selected.
The Sheath Gas Flow Rate readback is to the
right of the spin box. This readback displays
the actual flow rate (in arbitrary units).
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Parameter
Description
Aux Gas Flow Rate
Displays the setpoint APPI source auxiliary
gas flow rate (in arbitrary units). To change
the setpoint flow rate, click the arrows in the
Aux Gas Flow Rate spin box to increment
[up arrow] or decrement [down arrow] the
value. You can set the flow rate to any value
from 0 to 40 units. Alternatively, you can
enter a value in the spin box text field. The
mass spectrometer changes the flow rate
when you click Apply or with the Hot link
check box being selected.
The Aux Gas Flow Rate readback is to the
right of the spin box. This readback displays
the actual flow rate (in arbitrary units).
Sweep Gas Flow Rate
Displays the setpoint APPI source sweep gas
flow rate. To change the setpoint flow rate,
click the arrows in the Sweep Gas Flow Rate
spin box to increment [up arrow] or
decrement [down arrow] the value. You can
set the flow rate to any value from 0 to
10 units. Alternatively, you can enter a value
in the spin box text field. The mass
spectrometer changes the flow rate when you
click Apply or with the Hot link check box
being selected.
The Sweep Gas Flow Rate readback is to the
right of the spin box. This readback displays
the actual flow rate (in arbitrary units).
Discharge Voltage
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When APPI is selected as ionization method,
the actual discharge voltage displays ‘0’.
When either APCI or APCI+APPI is selected
as ionization method, the actual discharge
voltage displays APCI voltage readback
(absolute value, in kilovolts).
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Parameter
Description
Discharge Current
Displays the setpoint source discharge
current (in microamperes). To change the
setpoint discharge current, click the arrows
in the Discharge Current spin box to
increment [up arrow] or decrement [down
arrow] the value. You can set the discharge
current to any value from 0 to 80 μA. (A
typical value is 5 μA.) Alternatively, you can
enter a value in the spin box text field. The
mass spectrometer changes the discharge
current when you click Apply or with the
Hot link check box being selected.
Note When APPI is selected as ionization
method, changes in discharge current have
no effect. Discharge current changes are
applied only when either APCI or
APCI+APPI is selected as ionization
method. ▲
The Discharge Current readback is to the
right of the spin box. This readback displays
the actual discharge current (in
microamperes).
Capillary Temperature
Displays the setpoint APPI source heated
capillary temperature (in degrees Celsius). To
change the setpoint heated capillary
temperature, click the arrows in the
Capillary Temp spin box to increment [up
arrow] or decrement [down arrow] the value.
You can set the heated capillary temperature
to any value from 0.00 to 450.00 °C.
Alternatively, you can enter a value in the
spin box text field. The mass spectrometer
changes the heated capillary temperature
when you click Apply or with the Hot link
check box being selected.
The Capillary Temperature readback is to
the right of the spin box. This readback
displays the actual temperature (in degrees
Celsius) of the heated capillary.
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Parameter
Description
Capillary Voltage
Displays the setpoint APPI source heated
capillary voltage (in volts). To change the
setpoint heated capillary voltage, click the
arrows in the Capillary Voltage spin box to
increment [up arrow] or decrement [down
arrow] the value. You can set the heated
capillary voltage to any value from -140 to
+140 V. Alternatively, you can enter a value
in the spin box text field. The mass
spectrometer changes the heated capillary
voltage when you click Apply or with the
Hot link check box being selected. A
Capillary Voltage readback is not displayed.
Tube Lens Voltage
Displays the setpoint APPI source tube lens
voltage (in volts). To change the setpoint
tube lens voltage, click the arrows in the
Tube Lens spin box to increment [up arrow]
or decrement [down arrow] the value. The
values you can set the tube lens voltage to
vary with the mass of the ions being analyzed
and the polarity of the ions. Alternatively,
you can enter a value in the spin box text
field. The mass spectrometer changes the
tube lens voltage when you click Apply or
with the Hot link check box being selected.
A Tube Lens Voltage readback is not
displayed.
Skimmer Voltage
Displays the setpoint APPI source skimmer
voltage (in volts). You can set the skimmer
voltage to any value from -50 to +50 V. To
change the setpoint skimmer voltage, click
the arrows in the Skimmer Voltage spin box
to increment [up arrow] or decrement [down
arrow] the value. Alternatively, you can enter
a value in the spin box text field. The mass
spectrometer changes the skimmer voltage
when you click Apply or with the Hot link
check box being selected. A Skimmer
Voltage readback is not displayed.
Exactive Software Manual (P/N 1249910, Revision C)
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Parameter
Description
Vaporizer Temperature Displays the setpoint APPI source vaporizer
temperature (in degrees Celsius). To change
the setpoint vaporizer temperature, click the
arrows in the Vaporizer Temp. spin box to
increment [up arrow] or decrement [down
arrow] the value. You can set the vaporizer
temperature to any value from 0 to 500 °C.
Alternatively, you can enter a value in the
spin box text field. The mass spectrometer
changes the vaporizer temperature when you
click Apply or with the Hot link check box
being selected.
The Vaporizer Temperature readback is to
the right of the spin box. This readback
displays the actual temperature (in degrees
Celsius) of the vaporizer.
Ionization
Use this list box to select the ionization
method. The following options are available:
APCI
APCI alone
APPI
Photoionization
APCI + APPI
APCI in combination with APCI
•
•
•
Buttons
Apply
Sends all changes to the instrument.
Help
Displays the Help for this window.
Hot Link
Select the Hot link check box to allow
Exactive Tune to send any changes
immediately to the instrument. A green
frame around the parameter box indicates an
active hot link.
❖
To display this dialog box
Click the APPI source window title bar in the Instrument Control
window.
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Acquisition Window
Use the Acquisition window to enter parameters for acquiring and
storing scan data as well as to monitor the progress of the active
acquisition. See Figure 4-21.
Figure 4-21. Acquisition window
The Acquisition window has the following parameters:
Parameter
Description
Acquisition state
Displays the status of the current acquisition.
Progress
Displays the elapsed time of the current
acquisition.
File in use
Displays the name of the raw file to be acquired
to disk for the current sample. To display the file
in Qual Browser, click the
button.
This value is up to date even when Exactive
Tune is acquiring data under control of Xcalibur.
Destination file
Displays the full path of the folder where your
*.raw files will be saved. To change the path,
type the full path (Drive:\path) in the text box or
click the button to the right of the text box to
browse your directories and select the folder
where your *.raw files should be saved.
Note Saving raw files on network drives typically
causes problems. Preferably select a local path
(for example, C:\Xcalibur\data). ▲
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Parameter
Description
Method file
Displays the name of the instrument method
(*.meth) to be used during the current
acquisition. The tune file used in that
instrument method will be used for your scan
but other devices configured in that instrument
method will not be included. Type in the name
of the instrument method, or click the
button to the right of the text box to browse
your computer for an instrument method file
(typically saved in C:\Xcalibur\methods).
When the active acquisition is controlled by the
settings of the parameter Acquisitions time, this
parameter is not available. Instead, the text field
shows by time.
Thermo Fisher Scientific
Sample
Displays the name of the current sample. To
change the sample name, type the new name in
the text field.
Comment
Displays a comment on the current sample, if
available. To change the comment, type the new
name in the text field.
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Parameter
Description
Acquisition time
Displays the duration of the acquisition time.
Use the option buttons to select one of the
following settings:
•
Continuously
The acquisition, once it is started, will
continue until you stop (Stop button) or
pause (Pause button) it.
•
Scans
Specify the number of scans for the current
acquisition. You can set the number of scans
to any value from 1 to 10000.
To change this value, click the arrows in the
spin box to increment [up arrow] or
decrement [down arrow] the value.
Alternatively, enter a value in the spin box
text field.
•
Minutes
Specify the time in minutes for the current
acquisition. You can set the acquisition time
from 0.01 to 15000.00 minutes.
To change this value, click the arrows in the
spin box to increment [up arrow] or
decrement [down arrow] the value.
Alternatively, enter a value in the spin box
text field.
When the active acquisition is controlled by a
method file, this parameter is not available.
Instead, the text field shows by method.
On start
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Use the list box to set the start mode of the data
acquisition. The options are as follows:
•
don’t wait
Initiates acquisition of your raw file
immediately upon clicking Start in the
Acquisition window.
•
wait for contact closure
Initiates acquisition of your raw file when
Exactive Tune receives a contact closure
signal from your analog autosampler.
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Parameter
Description
After acquisition
Use the list box to set the instrument mode after
the data acquisition has stopped. The options
are as follows:
•
keep being on
The instrument remains On when the
current acquisition is completed.
•
enter standby mode
Sets the instrument to Standby when the
current acquisition is completed.
•
switch off
Switches Off the instrument when the
current acquisition is completed.
Buttons
Start / Stop
Allows starting and stopping data acquisition.
When no acquisition is in progress, Exactive
Tune displays Start. When an acquisition is in
progress, Exactive Tune displays Stop. To start
an acquisition, click Start. To stop an
acquisition, click Stop. To pause an acquisition,
click the Pause / Resume button.
Note No Exactive Tune controlled data
acquisition is possible if the instrument is
controlled by Xcalibur or Pathfinder. ▲
Pause / Resume
Allows pausing and resuming an acquisition in
progress. When no acquisition is in progress, the
button is inactive (gray). When an acquisition is
in progress, Exactive Tune displays Pause. When
an acquisition is paused, Exactive Tune displays
Resume. To pause an acquisition in progress,
click Pause. To resume an acquisition that is
paused, click Resume. To stop an acquisition in
progress, click the Start / Stop button.
Note The acquisition can be started by pressing
Resume if the Exactive mass spectrometer is
waiting for contact closure. ▲
Help
❖
Displays the Help for this window.
To display this window
Click the Acquisition window title bar in the Instrument Control
window.
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Tune Window
Use the Tune window of the tasks panel to optimize the tune of the mass
spectrometer. See Figure 4-22.
Figure 4-22. Tune window
Note Automatic tuning is disabled when in-source CID fragmentation
is on. To use the Tune window, disable source fragmentation in the Scan
Parameters window. ▲
The tuning procedure requires that you introduce tuning solution, or a
solution of your analyte of interest, into the mass spectrometer at a
steady rate for several minutes (or longer). You can introduce the
solution directly from the syringe pump or from the syringe pump into
the effluent of the LC by using a Tee union. Refer to the Exactive
Operating Manual for information.
Automatic tuning optimizes the following tune parameters:
•
Heated capillary voltage
•
Tube lens voltage
•
Skimmer voltage
•
Lens 0 and Lens 1 voltages
•
Gate lens voltage
•
Second multipole offset voltage
Note If the mass spectrometer is equipped with a HCD collision cell,
ensure that HCD fragmentation is not activated in the Fragmentation
dialog box. Otherwise, the tuning procedure comprises only
HCD relevant parameters. ▲
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The Tune window has the following parameters:
Parameter
Description
TIC
Select the TIC option button to perform an
automatic tuning of the MS detector using
the total ion current (TIC) intensity.
Mass
Select the Mass option button to perform an
automatic tuning of the MS detector using a
peak of interest at any specified
mass-to-charge ratio. When you select the
Mass option button, the spin box becomes
active. The spin box displays the
mass-to-charge ratio to optimize on. You
can set the mass-to-charge ratio to any value
from m/z 50 to m/z 4000.
To change this value, click the arrows in the
spin box to increment [up arrow] or
decrement [down arrow] the value.
Alternatively, enter a value in the spin box
text field.
Progress bar
Displays the elapsed percentage of the
current tuning procedure.
Buttons
Tune
Click Tune to start an automatic tuning of
the mass spectrometer. The instrument
needs to be in On state to start a tuning
procedure. Automatic tuning requires about
one minute.
When tuning is in progress, Exactive Tune
displays Stop.
Stop
Click Stop to stop a tuning in progress.
Help
Displays the Help for this window.
❖
To display this window
Click
Thermo Fisher Scientific
in the tasks panel.
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Tasks Panel
Calibrate Window
Use the Calibrate window of the tasks panel to perform an automatic
optimization of the calibration parameters. See Figure 4-23. Calibration
parameters are instrument parameters whose values do not vary with the
type of experiment.
Figure 4-23. Calibrate window
Note If the system was in Off mode before, it is necessary to put the
instrument into On mode for at least 90 minutes before a mass
calibration is performed. ▲
The calibrating procedure requires that you introduce calibration
solution into the mass spectrometer at a steady rate for several minutes
(or longer). You can introduce the solution directly from the syringe
pump or from the syringe pump into the effluent of the LC by using a
Tee union. Refer to the Exactive Operating Manual for information.
A complete calibration procedure comprises the following calibrations
(and evaluations):
•
Mass Resolution Dependency Calibration
•
Mass RF Amplitude Dependency Calibration
•
Mass Space Charge Dependency Calibration
•
Spectral Mass Accuracy Calibration
The Calibrate window has the following parameters:
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Parameter
Description
Positive Complete
Select this check box perform an automatic
calibration for all calibration parameters in the
positive ion mode.
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Tasks Panel
Parameter
Description
Negative Complete
Select this check box perform an automatic
calibration for all calibration parameters in the
negative ion mode.
Positive Mass
Select this check box perform an automatic
mass calibration in the positive ion mode.
Negative Mass
Select this check box perform an automatic
mass calibration in the negative ion mode.
Progress bar
Displays the elapsed percentage of the current
calibration procedure.
Buttons
Calibrate
Click Calibrate to start an automatic
calibration of the mass spectrometer. The
instrument needs to be in On state to start a
calibration. The duration of the automatic
calibration depends on the selected check
boxes; a complete automatic calibration
requires about four minutes.
When calibration is in progress, Exactive Tune
displays Stop.
Stop
Click Stop to stop a calibration in progress.
Help
Displays the Help for this window.
❖
To display this window
Click
Thermo Fisher Scientific
in the tasks panel.
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Tasks Panel
Evaluate Window
Use the Evaluate window of the tasks panel to perform an automatic
check of the instrument calibration. See Figure 4-24.
Figure 4-24. Evaluate window
The evaluation procedure requires that you introduce calibration
solution into the mass spectrometer at a steady rate for several minutes
(or longer). You can introduce the solution directly from the syringe
pump or from the syringe pump into the effluent of the LC by using a
Tee union. Refer to the Exactive Operating Manual for information.
A complete evaluation procedure comprises the following tests:
•
Mass Resolution Dependency Test
•
Mass RF Amplitude Dependency Test
•
Mass Space Charge Dependency Test
•
Spectral Mass Accuracy Test
The Evaluate window has the following parameters:
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Parameter
Description
Positive Complete
Select this check box perform an
automatic evaluation for all calibration
parameters in the positive ion mode.
Negative Complete
Select this check box perform an
automatic evaluation for all calibration
parameters in the negative ion mode.
Positive Mass
Select this check box perform an
automatic evaluation of the mass
calibration in the positive ion mode.
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Tasks Panel
Parameter
Description
Negative Mass
Select this check box perform an
automatic evaluation of the automatic
mass calibration in the negative ion
mode.
Progress bar
Displays the elapsed percentage of the
current evaluation procedure.
Buttons
Evaluate
Click Evaluate to start an automatic
evaluation of calibration parameters.
The instrument needs to be in On state
to start an evaluation.
When evaluation is in progress,
Exactive Tune displays Stop.
Stop
Click Stop to stop an evaluation in
progress.
Help
Displays the Help for this window.
❖
To display this window
Click
in the Tasks window.
Vacuum / Bakeout Window
The Vacuum / Bakeout window of the tasks panel reads back the
pressure values at the vacuum gauges and allows performing an
instrument bakeout. See Figure 4-25.
Figure 4-25. Vacuum / Bakeout window
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Tasks Panel
Note After the bakeout time has expired, the instrument requires a
cooling and stabilization time of about three hours. ▲
The Vacuum / Bakeout window has the following parameters:
Parameter
Description
Vacuum
Green LEDs indicate that the readback values are sufficient for
operating the Exactive mass spectrometer. If an LED indicates a
vacuum problem, use the instrument status window for error
diagnosis.
Fore vacuum
This readback displays the actual
pressure (in mBar) in the forevacuum
line and ion source region as read by the
Pirani gauge.
High vacuum
This readback displays the actual
pressure (in mBar) in the high vacuum
chamber as read by the ion gauge.
This parameter is visible only when the
ion gauge in the high vacuum chamber
is switched on. With exception of
standard users, users can switch on this
gauge by using the shortcut menu of
the Vacuum System node of the
instrument status window.
UHV
This readback displays the actual
pressure (in mBar) in the Orbitrap
chamber as read by the ion gauge.
Bakeout
Bakeout time
Enter the desired baking duration (in
hours) into the spin box. The range is 4
to 100 hours. When you click Bake
out, the mass spectrometer starts the
baking routine.
The baking script is stopped after the
preset duration. Click Stop to abort the
baking routine.
Note The instrument has to cool down
for another three hours before it can be
used. ▲
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Tasks Panel
Parameter
Description
Enter standby after Bakeout Select the check box to set the
instrument to standby mode after the
bakeout procedure is finished.
Progress bar
Displays the elapsed percentage of the
current baking procedure.
Bake out
Click Bake out to start the bakeout
routine. To stop a bakeout in progress,
click the Stop button.
Note Bakeout is possible only when the
instrument status is Off. ▲
Stop
Click Stop to abort the bakeout
routine.
Note The instrument has to cool down
for another three hours before it can be
used. ▲
Help
❖
Displays the Help for this window.
To display this window
Click
in the tasks
panel.
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Display Panel
Display Panel
The windows in the display panel provide real-time information about
the instrument status, Exactive Tune, or other programs.
The following windows are available:
•
Spectrum Window
•
Instrument Status Window
•
Messages Window
•
Analysis Graphs Window
•
Debug Messages Window
The spectrum window is always visible. The debug messages window is
not available for standard users.
Exactive Tune offers various ways to arrange windows in the display
panel:
❖
To display a window in the display panel
Choose the respective command in the Windows menu.
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❖
To hide a window in the display panel
•
Choose the respective command in the Windows menu.
•
Right-click the title bar of a window to display the shortcut menu.
Choose Hide.
❖
To change the position of a window in the display panel
•
Use the mouse to drag the window by its title bar to the new
location, which can be even outside the Exactive Tune window.
•
Within the display panel, you can dock the window to any one of
the four sides. While you drag the window, Exactive Tune displays
icons to indicate the available docking positions.
•
Right-click the title bar of a docked window to display the shortcut
menu. Choose Floating to undock the window.
•
Right-click the title bar of an undocked window to display the
shortcut menu. Choose Floating to dock the window to its last
docking position.
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Display Panel
Spectrum Window
The spectrum window displays real-time data generated during
calibration, tuning, and diagnostic tests. See Figure 4-26. The spectrum
window is always visible.
Figure 4-26. Spectrum window
The spectrum window allows using the mouse for zooming:
❖
To zoom in or out on a spectrum
•
Click and drag with the left mouse button (hand cursor) from
the beginning to the end of the portion you want to see
enlarged.
•
Alternatively, use the mouse wheel for zooming. Position the
mouse pointer within the spectrum and roll the wheel forward
to zoom in on the spectrum area.
•
To zoom in on the spectrum with respect to one axis only,
position the mouse pointer within the axis area and roll the
mouse wheel forward. Roll the wheel backward to zoom out.
•
To increase the zooming factor by two, keep the <Shift> key
pressed while using the mouse wheel.
To return to a display of the full spectrum, click the
the toolbar or choose Un-Zoom in the shortcut menu.
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Display Panel
Press the <Shift> key to enable mouse panning. When mouse panning
is active (mouse pointer changes to hand cursor), you can shift the
spectrum along the X-axis while keeping the left mouse button pressed.
The spectrum window has the following parameters:
Parameter
Description
Header
Scan #
The number of scans since the beginning of the
last acquisition (or since the last time the
MS detector was rebooted)
μS
Number of microscans
IT
Inject time (in milliseconds)
NL
Normalization level
Type
Scan type
The scan type information comprises ion
polarity, source type, fragmentation type and
energy (if active), and scan range. When the
acquisition is controlled by an instrument
method, the information includes the current
scan segment and the current scan event.
❖
To display this window
Choose Windows > Spectrum.
Toolbar
Use the buttons in the toolbar to manipulate the spectrum display.
The toolbar of the spectrum window has the following parameters:
Parameter
Description
Click to copy the current spectrum into the clipboard.
Click to plot the current spectrum.
You can view a print preview before the spectrum is
printed. In a Page Setup dialog box, you can set up
printer’s parameters (paper size and orientation, for
example).
Click to zoom in on the Y-axis (factor 2).
Click to zoom out on the Y-axis (factor 2).
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Display Panel
Parameter
Description
Click to normalize the Y scale: Exactive Tune always
displays the largest peak in the spectrum at full scale
(vertical scale = largest peak in spectrum).
Click to zoom in on the X-axis (factor 2).
Click to zoom out on the X-axis (factor 2).
Click to display the entire mass range.
Click to normalize the display (X-axis, Y-axis).
Click to set to fixed mode: the height of the Y-axis is set
equal to the height of the largest peak in the current
spectrum and remains fixed even if larger peaks occur.
Click to set the Y-axis to the height of the highest peak so
that the largest peak in the spectrum is always displayed
at full scale.
Click to set to creep mode: the Y scale of the mass
spectrum automatically increases if the peak intensity
increases, but does not decrease if the peak intensity
decreases.
Click to toggle between mouse panning and mouse
zooming:
• When mouse panning is active, you can shift the
spectrum along the X-axis while keeping the left
mouse button pressed (hand cursor).
• When mouse zooming is active, you can zoom in the
spectrum by using the mouse.
Shortcut Menu
Right-clicking on the spectrum window displays the shortcut menu. It
has the following commands:
Thermo Fisher Scientific
Command
Description
Save Image As
Saves the current graph as image file. A Save As
dialog opens and you can enter the file name,
file type, and the directory.
Un-Zoom
Reverts the zoom action.
Display options
Opens the Display Options dialog box.
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Display Panel
Instrument Status Window
The instrument status window displays real-time status information for
the instrument components. All parameters are arranged in a tree view.
See Figure 4-27. The Control node is not available for standard users.
Figure 4-27. Instrument Status window
In addition to showing numerical values of parameters, the instrument
status window uses icons to indicate the statuses of system components.
Thus, you can use the instrument status window for a quick error
diagnosis.
When expanded, some nodes provide shortcut menus that are displayed
when you right-click an item. The available commands depend on the
selected node and the user privileges. Generally, the shortcut menus
allow changing the current settings.
❖
To display this window
Choose Windows > Instrument Status.
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Display Panel
Messages Window
The messages window displays real-time information about the statuses
of the instrument, the control service, or other programs. See
Figure 4-28.
Figure 4-28. Messages window
For further analysis, you can copy the content of the messages window
to a text editor.
❖
To copy content from the messages window to a text editor
1. Select part of the content with the mouse, or
press <Ctrl> + <A> to select the complete content of the messages
window.
2. Press <Ctrl> + <C> to copy the text to the clipboard.
3. Open a document in the text editor.
4. Press <Ctrl> + <V> to insert the copied text into the document.
The messages window has the following parameters:
Parameter
Description
The messages are sorted with respect to time. To change the sort order,
click the respective table column header. To invert the sort order, click
again.
Priority
The message priority is indicated by symbols:
Info; status is normal / command successful
Warning; no user action required
Error; user action required
Fatal error; program cannot proceed
Source
Thermo Fisher Scientific
The message source is indicated by symbols:
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Display Panel
Parameter
Description
Message from Exactive Tune program
Message from instrument
Message from service
Time
Time and date of the message
Description Displays the message text.
❖
To display this window
Choose Windows > Messages.
Analysis Graphs Window
The analysis graphs window displays real-time data generated during
calibration, tuning, and diagnostic tests. See Figure 4-29. To save data
displayed in the window, choose Save Image As in the shortcut menu of
the window.
Figure 4-29. Analysis Graphs window
The analysis graphs window allows using the mouse for zooming:
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Display Panel
❖
To zoom in or out on an analysis graph
•
Click and drag with the left mouse button (hand cursor) from
the beginning to the end of the portion you want to see
enlarged.
•
Alternatively, use the mouse wheel for zooming. Position the
mouse pointer within the graph and roll the wheel forward to
zoom in on the graph area.
•
To zoom in on the graph with respect to one axis only, position
the mouse pointer within the axis area and roll the mouse wheel
forward. Roll the wheel backward to zoom out.
•
To increase the zooming factor by two, keep the <Shift> key
pressed while using the mouse wheel.
To return to a display of the full spectrum, click the
the toolbar or choose Un-Zoom in the shortcut menu.
button in
Press the <Shift> key to enable mouse panning. When mouse panning
is active (mouse pointer changes to hand cursor), you can shift the graph
along both axes while keeping the left mouse button pressed.
❖
To display this window
Choose Windows > Analysis Graphs.
Toolbar
The toolbar of the analysis graphs window has the following parameters:
Parameter
Description
Click to copy the current graph into the clipboard.
Click to plot the current graph.
You can view a print preview before the graph is printed.
In a Page Setup dialog box, you can set up printer’s
parameters (paper size and orientation, for example).
Click to normalize the display (X-axis, Y-axis).
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Display Panel
Shortcut Menu
Right-clicking on the analysis graphs window displays the shortcut
menu. It has the following commands:
Command
Description
Save Image As
Saves the current graph as image file. A Save As
dialog opens and you can enter the file name,
file type, and the directory.
Un-Zoom
Reverts the zoom action.
Debug Messages Window
The debug messages window displays messages that can be used during
method development. See Figure 4-30. The debug messages window is
not available for standard users.
Figure 4-30. Debug Messages window
For further analysis, you can copy the content of the debug messages
window to a text editor.
❖
To copy content from the debug messages window to a text editor
1. Select part of the content with the mouse, or
press <Ctrl> + <A> to select the complete content of the messages
window.
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Display Panel
2. Press <Ctrl> + <C> to copy the text to the clipboard.
3. Open a document in the text editor.
4. Press <Ctrl> + <V> to insert the copied text into the document.
The debug messages window has the following parameters:
Parameter
Description
The messages are sorted with respect to time. To change the sort order,
click the respective table column header. To invert the sort order, click
again.
Priority
The message priority is indicated by symbols:
Debugging message
Info; status is normal / command successful
Warning; no user action required
Error; user action required
Fatal error; program cannot proceed
Source
The message source is indicated by symbols:
Message from Exactive Tune program.
Message from instrument.
Message from service.
Time
Time and date of the message
Description Displays the message text.
❖
To display this window
Choose Windows > Debug Messages.
Shortcut Menu of the Debug Messages Window
The debug messages window has a shortcut menu that is displayed when
you right-click into the window. Use the commands of the shortcut
menu to configure the scope of the messages displayed in the window.
Click a command to activate it; click it again to deactivate it.
The following message priorities can be displayed:
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•
Debug
•
Log
•
Info
•
Warning
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Display Panel
•
Error
•
Fatal
For each message priority, the following message sources are available:
•
Instrument
•
Service
•
Application
A
icon in front of a message source shows that it is selected. A
icon in front of a message priority shows that it is shown for all three
message sources. A
icon in front of a message priority shows that it
is shown for one or two message sources.
In addition to the commands for configuring the content of the debug
messages window, the Clear list command allows removing the
complete content of the window.
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Dialog Boxes
Dialog Boxes
This section provides a reference to the dialog boxes in Exactive Tune.
Dialog Boxes Displayed from the Menu Bar
•
About Dialog Box
•
License Dialog Box
Dialog Boxes Displayed from the Toolbar
•
Syringe Pump Settings Dialog Box
Dialog Boxes Displayed from the Scan Parameters Window
•
Fragmentation Dialog Box
•
Scan Parameters History Dialog Box
•
Scan Range Dialog Box
Dialog Boxes for Editing Lock Masses
•
Collection Modification Dialog Box
•
Delete Lock Mass Collection Dialog Box
•
Lock Masses Dialog Box
•
Lock Mass Removal Dialog Box
•
Lock Mass Replacement Dialog Box
•
Name Change Dialog Box
•
New Lock Mass Collection Dialog Box
Dialog Boxes Displayed from the Spectrum Window
•
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Display Options Dialog Box
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Dialog Boxes
About Dialog Box
Use the About dialog box to display information about the instrument,
the current Exactive Tune version, and the active licenses. See
Figure 4-31. To copy the instrument identification to the clipboard,
click the
button.
Figure 4-31. About dialog box
The About dialog box has the following parameters:
Parameter
Description
Third party license
information
Displays a dialog box with information about
third party licenses used by Exactive Tune.
Buttons
OK
Saves your changes and closes the dialog box.
Add license
Displays the License dialog box.
Help
Displays the Help for this dialog box.
❖
To display this dialog box
Choose Help > About.
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Dialog Boxes
License Dialog Box
Use the License dialog box to enter licenses that activate additional
features. See Figure 4-32.
Figure 4-32. License dialog box
The License dialog box has the following parameters:
Parameter
Description
License key
Use the text box to enter the license key.
Buttons
OK
Saves your changes and closes the dialog box.
Cancel
Discards your changes and closes the dialog box.
Help
Displays the Help for this dialog box.
❖
To display this dialog box
1. Choose Help > About to display the About dialog box.
2. In the About dialog box, click Add license.
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Dialog Boxes
Syringe Pump Settings Dialog Box
Use the settings in this dialog box to specify parameters of the syringe
and the syringe pump. See Figure 4-33. Additionally, it allows manually
operating the syringe pump.
Figure 4-33. Syringe Pump Settings dialog box
Note With exception of standard users, users can select the syringe
pump type and enter parameters for the syringe pump in the instrument
status window. ▲
The Syringe Pump Settings dialog box has the following parameters:
Parameter
Description
Syringe type
Use this list box to specify the syringe
type (Hamilton, Unimetrics, or
Other). If you select Hamilton or
Unimetircs, you must specify the
volume of the syringe in the Volume
list box. If you select Other, you must
specify the inside diameter of the
syringe in the Syringe inner diameter
spin box.
Volume (μL)
Use this list box to specify the syringe
volume for Hamilton and Unimetrics
syringes. The acceptable values
depend on the syringe type:
•
•
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Hamilton:
0.5, 1, 2, 5, 10, 25, 50, 100, 250,
and 500 μL.
Unimetrics:
10, 25, 50, 100, 250, 500, 1000,
2500, 5000, 10000, 25000, and
50000 μL.
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Dialog Boxes
Parameter
Description
Syringe inner diameter (mm)
Use this spin box to specify the inside
diameter for syringes other than
Hamilton and Unimetrics syringes.
The acceptable range of values is 0.1
to 35 mm.
To change this value, click the arrows
in the spin box to increment [up
arrow] or decrement [down arrow] the
value. Alternatively, enter a value in
the spin box text field.
Flow rate (μL/min)
Use this spin box to specify the
volume of solvent solution passing
through the syringe pump per unit
time (in microliters per minute). The
acceptable range of values depends on
the selected syringe volume or syringe
inner diameter.
To change this value, click the arrows
in the spin box to increment [up
arrow] or decrement [down arrow] the
value. Alternatively, enter a value in
the spin box text field.
Buttons
Apply
Sends all changes to the instrument.
Help
Displays the Help for this window.
Manual Control
Sets the syringe pump to manual
control. Use the buttons on the
syringe pump to switch it on and off.
When the syringe pump is under
manual control, Exactive Tune
displays
Start
Switches on the syringe pump. When
the syringe pump is On, Exactive
Tune displays
Stop
.
Switches off the syringe pump. When
the syringe pump is Off, Exactive
Tune displays
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Dialog Boxes
❖
To display this dialog box
In the toolbar, right-click the
symbol.
Scan Parameters History Dialog Box
Use the Scan Parameters History dialog box to select from a list of recent
scans based upon short scan descriptions. See Figure 4-34. Select a scan
from the list to populate all scan parameters in the Scan Parameters
window with the parameters from that scan.
If the Hot link check box is selected in the Scan Parameters window,
selecting another list item immediately changes the instrument
parameters.
Figure 4-34. Scan Parameters History dialog box
❖
To display this dialog box
In the Scan Parameters window, click the History field.
Scan Range Dialog Box
Use the Scan range dialog box to specify the scan range of the data
acquisition. See Figure 4-35. The scan range affects the amount of
stored and transmitted data.
Figure 4-35. Scan range dialog box
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Dialog Boxes
Use he Scan Range dialog box to set either minimum and maximum or
center and width of the scan range. If you change one pair of values, the
other pair is changed accordingly.
Note The ratio for maximum-to-minimum should not exceed 20. If
necessary, Exactive Tune will correct the settings automatically. ▲
The Scan range dialog box has the following parameters:
Parameter
Description
Minimum
Use this spin box to select the minimum value for the
scan range (in mass-to-charge ratio units) used during
the currently selected scan event.
To change the value, click the arrows in the spin box
to increment [up arrow] or decrement [down arrow]
the value. You can enter any value from 50.0 to
3999.9. The default value is 120.
Maximum
Use this spin box to select the maximum value for the
scan range (in mass-to-charge ratio units) used during
the currently selected scan event.
To change the value, click the arrows in the spin box
to increment [up arrow] or decrement [down arrow]
the value. You can enter any value from 50.1 to
4000.0. The default value is 2000.
Center
Use this spin box to select the center mass (in
mass-to-charge ratio units) of the scan range.
To change the value, click the arrows in the spin box
to increment [up arrow] or decrement [down arrow]
the value. You can enter any value from 50.1 to
4000.0. The default value is 1060.
Width
Use this spin box to select the width of the scan range
(in mass-to-charge ratio units) used during the
currently selected scan event.
To change the value, click the arrows in the spin box
to increment [up arrow] or decrement [down arrow]
the value. You can enter any value from 0.1 to
3800.0. The default value is 1880.0.
❖
To display this dialog box
In the Scan Parameters window, click the Scan range field.
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Dialog Boxes
Fragmentation Dialog Box
Use the Fragmentation dialog box to activate a fragmentation with
in-source CID or the HCD collision cell. You can specify the
fragmentation voltages to be used. See Figure 4-36.
Figure 4-36. Tune – Fragmentation dialog box
The parameters of this dialog box are available only when the respective
features are installed.
The Fragmentation dialog box has the following parameters:
Parameter
Description
In-source CID
Activates the in-source CID.
To change the CID collision energy, click the
arrows in the spin box to increment [up arrow] or
decrement [down arrow] the value. You can set the
CID collision energy to any value from 0.1 to
100 eV. Default is 25.0 eV.
Note Automatic tuning is disabled when in-source
CID fragmentation is on. To use automatic tuning,
clear this check box. ▲
HCD Gas On
Activates the HCD collision gas flow. The HCD
check box becomes available, which allows
activating the HCD collision cell.
HCD
Activates the HCD collision cell. This check box
becomes available when the HCD Gas On check
box is selected.
To change the HCD collision energy, click the
arrows in the spin box to increment [up arrow] or
decrement [down arrow] the value. You can set the
HCD collision energy to any value from 10 to
200 eV. Default is 25.0 eV.
Note When HCD fragmentation is on, automatic
tuning comprises only HCD relevant parameters. ▲
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❖
To display this dialog box
In the Scan Parameters window, click into the Fragmentation field.
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Collection Modification Dialog Box
Use this dialog box to modify a lock mass collection by importing lock
masses from an .xml file See Figure 4-39. This dialog appears only when
the .xml file contains information about lock mass collections that
differs from the available lock mass collections.
Figure 4-37. Collection Modification dialog box
The Collection Modification dialog box has the following parameters:
Parameter
Description
OK
Saves your changes and closes the dialog box. The lock
mass collection is updated with the data contained in the
.xml file.
Cancel
Discards your changes and closes the dialog box.
Help
Displays the Help for this dialog box.
❖
To display this dialog box
1. Choose Import > Merge with file content in the shortcut menu of
the Lock Masses dialog box.
2. In the file selection dialog box, select an .xml file to import from.
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Dialog Boxes
Lock Masses Dialog Box
Use the Lock Masses dialog box to edit lock mass lists. See Figure 4-38.
The table shows all available lock masses. Lock mass collections store
information about lock mass usage.
Figure 4-38. Tune – Lock Masses dialog box
The Lock Masses dialog box has the following parameters:
Parameter
Description
Lock mass lists
Lock mass lists
Use the list box to select an existing lock mass
collection.
Displays the New Lock Mass Collection dialog box
where you can enter the name for a a new lock
mass collection.
Deletes the active lock mass collection. The lock
masses themselves are still available.
This button is not available when no lock mass
collection is selected.
Displays the Name Change dialog box where you
can edit the name of the active lock mass
collection.
This button is not available when no lock mass
collection is selected.
Available lock masses
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Parameter
Description
The table displays the properties of the available lock masses and
whether they are used in the selected lock mass collection. To change
the sort order, click the respective table column header. To invert the
sort order, click again.
Lock mass table
•
•
Use
Select the check box to use the lock mass. A
indicates that the lock mass is used in the active
lock mass collection. The lock mass is displayed
in the Lock masses field of the Scan Parameters
window.
Polarity
Click the symbol to change the polarity of the
lock mass.
Note During a scan, the Exactive mass
spectrometer uses only the lock masses with a
polarity that matches the active ion mode. ▲
•
•
m/z
Enter the mass of the lock mass into the field
(with a maximum of five decimals).
Comment
Enter a comment for the lock mass into the
field. This field is optional.
Creates a new lock mass.
Deletes the selected lock masses.
❖
To display this dialog box
In the Scan Parameters window, click into the Lock Masses field.
Shortcut Menu of the Lock Masses dialog box
The Lock Masses dialog box has a shortcut menu that is displayed when
you right-click into the dialog box.
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Dialog Boxes
It has the following commands:
Command
Description
Select all masses in use
Selects all masses used in the active lock
mass collection.
This command is not available when no
lock mass is used.
Import > Merge with
clipboard
Appends the content of the clipboard to
the available lock masses.
Note The clipboard stores lock mass data as
tabulator-separated text files. When the
data in the clipboard are not in this format,
the command is not available. ▲
Import > Replace by
clipboard
Replaces the available lock masses by the
content of the clipboard.
Note The clipboard stores lock mass data as
tabulator-separated text files. When the
data in the clipboard are not in this format,
the command is not available. ▲
Import > Merge with file Opens a dialog box so that you can select a
content
.csv, .txt, or .xml file that contains a list of
lock masses. The content of the file is
appended to the available lock masses.
See Exporting and Importing Lock Masses
for information about the format of lock
mass files.
Import > Replace by file
content
Opens a dialog box so that you can select a
.csv, .txt, or .xml file that contains a list of
lock masses. All available lock masses are
replaced by the masses contained in the
imported file. The present lock masses are
removed from all existing lock mass lists.
You have to confirm your action in the
Lock mass replacement dialog box.
See Exporting and Importing Lock Masses
for information about the format of lock
mass files.
Thermo Fisher Scientific
Export > Copy selected
to clipboard
Copies the data of the selected lock mass to
the clipboard.
Export > Copy all to
clipboard
Copies the data of all available lock masses
to the clipboard.
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Command
Description
Export > Copy selected
to file
Opens the dialog box, where you can save
the data of the selected lock mass(es) as a
.csv, .txt, or .xml file.
See Exporting and Importing Lock Masses
for information about the format of lock
mass files.
Export > Copy all to file
Opens the dialog box, where you can save
the data of all available lock masses as a
.csv, .txt, or .xml file.
See Exporting and Importing Lock Masses
for information about the format of lock
mass files.
Lock Mass Removal Dialog Box
Use this dialog box to delete one or more lock masses that are selected in
the Lock Masses dialog box. See Figure 4-39.
Figure 4-39. Lock Mass Removal dialog box
The Lock Mass Removal dialog box has the following parameters:
Parameter
Description
OK
Saves your changes and closes the dialog box. The lock
masses are now removed from the table in the Lock
Masses dialog box.
Cancel
Discards your changes and closes the dialog box.
Help
Displays the Help for this dialog box.
❖
To display this dialog box
In the Lock Masses dialog box, click the
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Dialog Boxes
Lock Mass Replacement Dialog Box
Use this dialog box to replace all available lock masses by masses
contained either in a .csv, .txt, or .xml file or in the clipboard. See
Figure 4-39.
Figure 4-40. Lock Mass Replacement dialog box
The Lock Mass Replacement dialog box has the following parameters:
Parameter
Description
OK
Removes the lock masses and replaces them by the
imported lock masses. The present lock mass collections
become void.
Cancel
Closes the dialog box.
Help
Displays the Help for this dialog box.
❖
To display this dialog box
Choose Import > Replace by file content or Import > Replace by
clipboard in the shortcut menu of the Lock Masses dialog box.
New Lock Mass Collection Dialog Box
Use this dialog box to enter a name for the lock mass collection that is
displayed in the Lock Masses dialog box. See Figure 4-41.
Figure 4-41. New Lock Mass Collection dialog box
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The New Lock Mass Collection dialog box has the following
parameters:
Parameter
Description
Name of lock mass Use this text field to enter the name for the new
collection
lock mass collection.
Buttons
OK
Saves your changes and closes the dialog box.
The name of the lock mass collection is now
displayed in the list box of the Lock Masses
dialog box.
Cancel
Discards your changes and closes the dialog box.
Help
Displays the Help for this dialog box.
❖
To display this dialog box
In the Lock Masses dialog box, click the
button.
Delete Lock Mass Collection Dialog Box
Use this dialog box to delete an existing lock mass collection. See
Figure 4-42. The lock masses themselves are not deleted.
Figure 4-42. Delete Lock Mass Collection dialog box
The Delete Lock Mass Collection dialog box has the following
parameters:
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Parameter
Description
OK
Saves your changes and closes the dialog box. The name
of the lock mass collection is now removed from the list
box of the Lock Masses dialog box.
Cancel
Discards your changes and closes the dialog box.
Help
Displays the Help for this dialog box.
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Dialog Boxes
❖
To display this dialog box
In the Lock Masses dialog box, click the
button.
Name Change Dialog Box
Use this dialog box to change the name of an existing lock mass
collection. See Figure 4-43.
Figure 4-43. Name Change Dialog Box
The Name Change dialog box has the following parameters:
Parameter
Description
Name of lock mass Use this text field to enter the new name for the
collection
lock mass collection.
Buttons
OK
Saves your changes and closes the dialog box.
The name of the lock mass collection is now
displayed in the list box of the Lock Masses
dialog box.
Cancel
Discards your changes and closes the dialog box.
Help
Displays the Help for this dialog box.
❖
To display this dialog box
In the Lock Masses dialog box, click the
Thermo Fisher Scientific
button.
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Display Options Dialog Box
Use this dialog box to modify the appearance of the displayed mass
spectrum in the spectrum window. See Figure 4-44.
Figure 4-44. Display Options Dialog Box
The Display Options dialog box has the following parameters:
Parameter
Description
Decimal places for m/z Use this list box to set how many decimal
places of precision are shown when mass
positions are annotated on mass spectra. The
valid range is 0 to 5.
Show resolution
Select this check box to have the Exactive
mass spectrometer annotate mass peaks with
the mass resolution.
Show charge state
Select this check box to have the Exactive
mass spectrometer annotate mass peaks with
the charge state.
Show flags
Select this check box to have the Exactive
mass spectrometer indicate peaks that are
contained in the active lock mass collection.
Note The scan parameters window must
show entries for lock masses. ▲
Buttons
OK
Saves your changes and closes the dialog box.
Help
Displays the Help for this dialog box.
❖
To display this dialog box
In the shortcut menu of the spectrum window, choose Display
options.
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Chapter 5
Procedures in Exactive Tune
This chapter describes procedures that you may need when using
Exactive Tune.
Contents
Thermo Fisher Scientific
•
Using Lock Masses and Lock Mass Collections
•
Performing a System Bakeout
•
Changing Default Settings of Exactive Tune
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5-1
Procedures in Exactive Tune
Using Lock Masses and Lock Mass Collections
Using Lock Masses and Lock Mass Collections
sectionThis topic provides instructions for using lock masses and lock
mass collections.
The following topics are available:
•
Adding a Lock Mass
•
Deleting Lock Masses
•
Exporting and Importing Lock Masses
•
Creating a new Lock Mass Collection
•
Renaming a Lock Mass Collection
•
Adding a Lock Mass to a Lock Mass Collection
•
Removing a Lock Mass from a Lock Mass Collection
•
Deleting a Lock Mass Collection
❖
To add a lock mass
Adding a Lock Mass
1. In the Lock Masses dialog box, click the
button. A new row
appears at the end of the lock mass table. See Figure 5-1.
Figure 5-1.
Adding a new lock mass
2. Enter the data for the new lock mass into the new table row:
a. Select the Use check box if you want to use the new lock mass in
the active lock mass collection.
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Procedures in Exactive Tune
Using Lock Masses and Lock Mass Collections
b. Click the cell in the Polarity column until the correct sign
appears:
for positive or
for negative.
c. Enter the m/z value for the new lock mass (with a maximum of
five decimals).
d. Optionally, enter a comment for the new lock mass.
The new lock mass is now available to be used.
Deleting Lock Masses
❖
To delete lock masses
1. In the Lock Masses dialog box, select one lock mass or several lock
masses:
•
To select a single lock mass, click into the respective table row.
•
To select adjacent lock masses, click the first table row. Then
hold down the <Shift> key while you click the last row.
•
To select nonadjacent lock masses, click the first table row. Then
hold down the <Ctrl> key while you click the other rows that
you want to add to the selection.
2. Click the
button. The Lock Mass Removal dialog box appears
and requests your confirmation for deleting the listed lock masses.
3. Click OK to confirm your input and to close the dialog box. All
selected lock masses are removed from the list in the Lock Masses
dialog box.
Exporting and Importing Lock Masses
Exactive Tune allows exporting lock mass data to the clipboard or to a
file. Other applications can then use the data. You can also copy the
export files to other computers where Exactive Tune is installed. So you
can reuse the lock masses without having to recreate them. To reuse the
lock masses, import the data either from the clipboard or from a lock
mass file.
With a spreadsheet, a text editor, or an XML editor, you can create lock
mass files even without using Exactive Tune.
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Procedures in Exactive Tune
Using Lock Masses and Lock Mass Collections
Lock Mass Files
Exactive Tune uses the following file formats for exporting and
importing lock mass data:
•
Comma-separated value lists (.csv)
•
Tabulator-separated text files (.txt)
•
XML files (.xml)
Lock mass data are stored in the following order:
1. Usage status: True for used, False for unused
2. Ion polarity: positive mode or negative mode
3. m/z: up to five decimals
4. Comment: optional
The clipboard stores lock mass data as tabulator-separated text files. In
contrast to . csv and .txt files, .xml files additionally store information
about lock mass collections and lock mass usage.
Exporting Lock Masses
Exactive Tune allows exporting lock mass data to the clipboard or to a
file.
❖
To export selected lock masses to the clipboard
1. In the Lock Masses dialog box, select the lock masses you want to
export:
•
To select a single lock mass, click into the respective table row.
•
To select adjacent lock masses, click the first table row. Then
hold down the <Shift> key while you click the last row.
•
To select nonadjacent lock masses, click the first table row. Then
hold down the <Ctrl> key while you click the other rows that
you want to add to the selection.
2. Right-click into the dialog box to display the shortcut menu.
3. Choose Export > Copy selected to clipboard to copy the selected
lock mass to the clipboard.
❖
To export all lock masses to the clipboard
1. In the Lock Masses dialog box, right-click into the dialog box to
display the shortcut menu.
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Procedures in Exactive Tune
Using Lock Masses and Lock Mass Collections
2. Choose Export > Copy all to clipboard to copy all available lock
mass to the clipboard.
❖
To export some lock masses to a file
1. In the Lock Masses dialog box, select the lock masses you want to
export:
•
To select a single lock mass, click into the respective table row.
•
To select adjacent lock masses, click the first table row. Then
hold down the <Shift> key while you click the last row.
•
To select nonadjacent lock masses, click the first table row. Then
hold down the <Ctrl> key while you click the other rows that
you want to add to the selection.
2. Right-click into the dialog box to display the shortcut menu.
3. Choose Export > Copy selected to file to open the file selection
dialog box. See Figure 5-2.
Figure 5-2.
Selecting the lock mass export file
a. Browse to the destination of the export file.
b. Select the format of the export file.
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Procedures in Exactive Tune
Using Lock Masses and Lock Mass Collections
c. Enter a new name for the export file or select an existing file.
d. Click Save to export the selected lock masses to the file. If you
want to overwrite an existing file, you have to confirm your
action in a dialog box. The file selection dialog box is closed.
❖
To export all lock masses to a file
1. In the Lock Masses dialog box, right-click into the dialog box to
display the shortcut menu.
2. Choose Export > Copy all to file to open the file selection dialog
box. See Figure 5-3.
Figure 5-3.
Selecting the lock mass export file
a. Browse to the destination of the export file.
b. Select the format of the export file.
c. Enter a new name for the export file or select an existing file.
d. Click Save to export the lock masses to the file. If you want to
overwrite an existing file, you have to confirm your action in a
dialog box. The file selection dialog box is closed.
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Procedures in Exactive Tune
Using Lock Masses and Lock Mass Collections
Importing Lock Masses
Exactive Tune allows importing lock mass data from the clipboard or
from a file. The imported lock masses either are added to the present
lock masses or they replace them.
❖
To add lock masses from the clipboard
1. Copy lock mass data in an appropriate format to the clipboard. See
Lock Mass Files for information about the requirements.
2. In the Lock Masses dialog box, right-click into the dialog box to
display the shortcut menu.
3. Choose Import > Merge with clipboard to import the lock mass
data from the clipboard to the lock mass table.
Note The clipboard stores lock mass data as tabulator-separated text
files. When the data in the clipboard are not in this format, the
command is not available. ▲
4. The lock mass list in the Lock Masses dialog box displays additional
rows for the imported lock masses.
❖
To add lock masses from a file
1. In the Lock Masses dialog box, right-click into the dialog box to
display the shortcut menu.
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Procedures in Exactive Tune
Using Lock Masses and Lock Mass Collections
2. Choose Import > Merge with file content to open the file selection
dialog box. See Figure 5-4.
Figure 5-4.
Selecting the lock mass import file
a. Browse to the destination of the import file.
b. Select the format of the import file.
c. Select one of the displayed files.
d. Click Open to import the lock masses to Exactive Tune. The
dialog box is closed.
3. If you are importing an .xml file that contains information about
lock mass collections that differs from the present lock mass
collections, the Collection modification dialog is displayed. Click
OK to confirm the operation and to close the dialog box.
4. The lock mass list in the Lock Masses dialog box displays additional
rows for the imported lock masses.
❖
To replace all lock masses by clipboard data
1. Copy lock mass data in an appropriate format to the clipboard. See
Lock Mass Files for information about the requirements.
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Procedures in Exactive Tune
Using Lock Masses and Lock Mass Collections
2. In the Lock Masses dialog box, right-click into the dialog box to
display the shortcut menu.
3. Choose Import > Replace by clipboard to import the lock mass
data from the clipboard to the lock mass table.
Note The clipboard stores lock mass data as tabulator-separated text
files. When the data in the clipboard are not in this format, the
command is not available. ▲
4. The Lock Mass Replacement dialog box is displayed. Click OK to
confirm the import.
5. The Lock Mass Replacement dialog box is closed. The lock mass list
in the Lock Masses dialog box displays only the imported lock
masses.
❖
To replace all lock masses from a file
1. In the Lock Masses dialog box, right-click into the dialog box to
display the shortcut menu.
2. Choose Import > Replace by file content.
3. The Lock Mass Replacement dialog box is displayed. Click OK to
confirm the import.
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Procedures in Exactive Tune
Using Lock Masses and Lock Mass Collections
4. The Lock Mass Replacement dialog box is closed. The file selection
dialog box is displayed. See Figure 5-5.
Figure 5-5.
Selecting the lock mass import file
a. Browse to the destination of the import file.
b. Select the format of the import file.
c. Select one of the displayed files.
d. Click Open to import the lock masses to Exactive Tune. The
dialog box is closed.
5. The lock mass list in the Lock Masses dialog box displays only the
imported lock masses.
If you have imported lock mass data from an .xml file that contained
information about lock mass collections and lock mass usage, the
dialog box displays the corresponding information.
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Procedures in Exactive Tune
Using Lock Masses and Lock Mass Collections
Creating a new Lock Mass Collection
❖
To create a lock mass collection
1. In the Lock Masses dialog box, click the
button.
2. In the New Lock Mass Collection dialog box, enter a name for the
new lock mass collection. See Figure 5-6.
Figure 5-6.
Creating a lock mass collection
3. Click OK to confirm your input and to close the dialog box.
4. The name of the new lock mass collection appears in the list box of
the Lock Masses dialog box.
Renaming a Lock Mass Collection
❖
To rename a lock mass collection
1. In the Lock Masses dialog box, select an existing lock mass
collection in the list box.
2. Click the
button. The Name Change dialog box is displayed.
See Figure 5-7.
Figure 5-7.
Changing the name of a lock mass collection
3. In the text field, replace the old name of the lock mass collection
with the new name.
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Procedures in Exactive Tune
Using Lock Masses and Lock Mass Collections
4. Click OK to confirm your input and to close the dialog box.
5. In the Lock Masses dialog box, the new lock mass collection is
displayed in the list box.
Adding a Lock Mass to a Lock Mass Collection
❖
To add a lock mass to a lock mass collection
1. In the Lock Masses dialog box, select an existing lock mass
collection in the list box.
2. Select the Use check box in the table row of the lock mass.
3. A indicates that the lock mass is used in the active lock mass
collection.
Removing a Lock Mass from a Lock Mass Collection
❖
To remove a lock mass from a lock mass collection
1. In the Lock Masses dialog box, select an existing lock mass
collection in the list box.
2. Clear the Use check box in the table row of the lock mass.
3. A indicates that the lock mass is not used in the active lock mass
collection.
Deleting a Lock Mass Collection
❖
To delete a lock mass collection
1. In the Lock Masses dialog box, select an existing lock mass
collection in the list box.
1. Click the
button.
2. In the Delete Lock Mass Collection dialog box, click OK to confirm
your action and to close the dialog box.
3. The name of the lock mass collection is removed from the list box of
the Lock Masses dialog box.
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Procedures in Exactive Tune
Performing a System Bakeout
Performing a System Bakeout
This topic describes the system bakeout of the Exactive mass
spectrometer. The bakeout procedure removes unwanted gases or
molecules (collected or remaining) from the high vacuum region of the
instrument. Ions can collide with those gases or molecules resulting in
lower overall sensitivity. Therefore, we recommend baking out the
instrument if the ultra high vacuum decreases noticeable during routine
operation.
Note Bakeout is mandatory after maintenance or service work is
performed in the analyzer region where the system is vented. You should
bake out an instrument that has been vented for at least twelve hours
before you can start using it again. ▲
In case the system has been vented during a power failure, it is necessary
to bake out the system to obtain the operating vacuum.
❖
To perform a system bakeout
1. Place the system in Standby condition. (See image in margin.)
2. Put the electronics service switch at the power control panel of the
Exactive mass spectrometer into the Service Mode position.
3. In the tasks panel, click
display the Vacuum / Bakeout window.
to
4. Enter the desired baking duration (in hours) into the spin box. The
range is 4 to 100 hours. See Figure 5-8.
Figure 5-8.
Thermo Fisher Scientific
Vacuum / Bakeout window
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Procedures in Exactive Tune
Performing a System Bakeout
5. Click Bake out. A dialog box shows the duration of the baking
procedure. See Figure 5-9. Click Yes to confirm the message.
Figure 5-9.
Bakeout message box
6. The message box disappears and the baking procedure starts. The
instrument indicates the active bakeout procedure by a flashing
Vacuum LED at the front side. Additionally, Exactive Tune displays
a corresponding message box. See Figure 5-10.
Figure 5-10. Message box: Vacuum Bakeout active
7. The baking of the instrument stops after the preset duration. The
Vacuum LED keeps flashing until the cooling and stabilization time
(of about 3 hours) is finished.
Click Stop in the Vacuum / Bakeout window to abort the baking
routine before the preset time.
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Procedures in Exactive Tune
Changing Default Settings of Exactive Tune
Changing Default Settings of Exactive Tune
With exception of standard users, users can use the instrument status
window to change default settings of Exactive Tune.
The following topics are available:
•
Displaying the High Vacuum Readback
•
Calibrating with Custom Mass Lists
•
Entering Parameters for the Syringe Pump
•
Changing the Settings for the Performance Status Check
Displaying the High Vacuum Readback
The High Vacuum readback in the Vacuum / Bakeout window is visible
only when the ion gauge in the high vacuum chamber is switched on.
With exception of standard users, users can switch on this gauge
manually.
❖
To switch on the High Vacuum readback in the Vacuum / Bakeout
window
1. Click
in the tasks
panel to display the Vacuum / Bakeout window.
2. If the instrument status window is not visible, choose Windows >
Instrument Status.
3. In the instrument status window, click Instrument > Vacuum
System.
4. Right-click the High Vacuum parameter to display the shortcut
menu.
5. Choose Turn on to switch on the ion gauge in the high vacuum
chamber.
6. The Vacuum / Bakeout window now displays the High Vacuum
readback.
To extend the lifetime of the ion gauge in the high vacuum chamber, it
is switched off again after a preset time of about thirty minutes.
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Procedures in Exactive Tune
Changing Default Settings of Exactive Tune
Calibrating with Custom Mass Lists
With exception of standard users, users can run mass calibration with
custom mass lists for both ion modes. Each list can contain up to ten
masses. This section describes how to create user-defined mass lists and
how to calibrate the instrument with it.
Editing User-Defined Mass Lists
❖
To display a user-defined mass list
1. If the instrument status window is not visible, choose Windows >
Instrument Status.
2. In the instrument status window, click Instrument > Control >
Procedures > User Mass List. Separate entries for positive ions and
negative ions display summaries of the mass lists with the number of
defined masses (6, for example) and the covered mass range
([138.1 - 1622.0], for example). See Figure 5-11.
Figure 5-11. Instrument status window – User Mass List node
3. To display a mass list, double-click the respective summary (Positive
ions, for example) to expand it. See Figure 5-12. The instrument
status window displays a list with all available user-defined masses
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Procedures in Exactive Tune
Changing Default Settings of Exactive Tune
for the active ion mode. The list entries are sorted in ascending
order.
List summary
List entries
Figure 5-12. Editing a user-defined mass list
❖
To delete a mass from the list
1. Right-click a list item to display the shortcut menu.
2. Choose Clear entry. The mass is removed from the list.
❖
To add a new mass to the list
1. Right-click either the list summary or an empty list item to display
the shortcut menu.
2. In the shortcut menu, click into the mass input field.
3. Enter the new theoretical mass into the input field.
4. Click the <Enter> key to confirm your input and to close the
shortcut menu.
❖
To delete all masses in the list
1. Choose Clear list in the shortcut menu of the list summary.
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Procedures in Exactive Tune
Changing Default Settings of Exactive Tune
❖
Adding active lock masses to the user-defined mass list
1. If necessary, use the Lock Masses dialog box to select the individual
lock masses or a lock mass collection that you want to use as
calibration masses.
2. Do one of the following:
•
To add lock masses of one polarity only, right-click the
respective summary (Positive ions, for example).
•
To add lock masses of both polarities, right-click the User Mass
List line.
3. In the shortcut menu, choose Load from active lock masses.
After each action, the mass list summary is updated and the list items are
automatically sorted in ascending order. The User Mass List line
displays the word Modified.
❖
To reset the user-defined mass lists
1. Right-click the User Mass List line to display the shortcut menu.
2. Choose Set to calmix to fill both mass lists with the theoretical
masses produced by the calibration solutions that are available for
the Exactive mass spectrometer. The User Mass List line displays the
word Calmix.
Refer to the Exactive Operating Manual for information about
calibration solutions.
Calibrating with User-Defined Mass Lists
❖
To calibrate with user-defined mass lists
1. If necessary, create a custom mass list as described in “Editing
User-Defined Mass Lists” on page 5-16.
2. If the instrument status window is not visible, choose Windows >
Instrument Status.
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Procedures in Exactive Tune
Changing Default Settings of Exactive Tune
3. In the instrument status window, click Instrument > Control >
Procedures > Calibrate. Separate entries for positive ion mode and
negative ion mode are displayed. See Figure 5-13.
Figure 5-13. Instrument status window – Calibrate node
4. To switch the calibration to using the custom mass list, right-click
an entry [Mass calibration (pos), for example] to display the
shortcut menu.
5. Choose User in the Mass List list box. See Figure 5-14.
Figure 5-14. Selecting a custom mass list for calibration
6. Perform the calibration of the Exactive mass spectrometer as
described in the Exactive QuickStart Guide.
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Procedures in Exactive Tune
Changing Default Settings of Exactive Tune
Entering Parameters for the Syringe Pump
The syringe contact of the Exactive mass spectrometer allows controlling
established syringe pumps by Exactive Tune by means of the
RS-232 serial interface. Suitable syringe pumps are the Chemyx
Fusion 100 pump (available from Thermo Fisher Scientific) and the
Harvard Apparatus Model 11 Plus Advanced pump. With exception of
standard users, users can select the syringe pump type and enter
parameters for the syringe pump in the instrument status window
❖
To enter parameters for the syringe pump
1. If the instrument status window is not visible, choose Windows >
Instrument Status.
2. In the instrument status window, click Instrument > System >
Configuration settings > Peripherals. The Peripherals node
displays parameters for the syringe pump. See Figure 5-15.
Figure 5-15. Instrument status window – Peripherals node
3. To change the settings for a parameter, right-click the parameter
entry to display the shortcut menu. If necessary, change the values of
the following parameters:
•
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Syringe Pump Controller Type: In the list box, select either Type
Harvard (for Harvard Apparatus Model 11 Plus Advanced
pump) or Type Chemyx (for Chemyx Fusion 100 pump).
Thermo Fisher Scientific
Procedures in Exactive Tune
Changing Default Settings of Exactive Tune
•
Syringe Type Harvard Serial Com Speed: Enter the baud rate for
the interface into the input field. Available options are 1200,
2400, 4800, 9600, and 19200 bauds. Press the <Enter> key to
confirm your input.
•
Syringe Type Chemyx Serial Com Speed: Enter the baud rate for
the interface into the input field. Available options are 1200,
2400, 4800, 9600, and 19200 bauds. Press the <Enter> key to
confirm your input.
Refer to the manual that came with the syringe pump for the correct
baud rate.
Changing the Settings for the Performance Status Check
By default, the performance status icon on the toolbar turns yellow
25 hours after the last successful mass calibration or check. With
exception of standard users, users can change this value in the System
node of the instrument status window according to their mass accuracy
requirements.
❖
To change the settings for the performance status check
1. If the instrument status window is not visible, choose Windows >
Instrument Status.
2. In the instrument status window, click Instrument > System >
Configuration settings > Performance Check. The Mass
calibration due time (h) field displays the current validity period of
the mass calibration (25 hours, for example). See Figure 5-16.
Figure 5-16. Instrument status window – Performance Check node
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Procedures in Exactive Tune
Changing Default Settings of Exactive Tune
3. To change the value, right-click the number in the text field to
display the shortcut menu.
4. In the Set text field, enter the new validity period (40, for example).
See Figure 5-17. You can enter a value between 1 and 500 hours.
Figure 5-17. Changing the calibration validity period
5. Press the <Enter> key to confirm your input. The shortcut menu
disappears and the new value is displayed in the instrument status
window.
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Chapter 6
Reference Information
This chapter provides reference information for the following:
Contents
Thermo Fisher Scientific
•
Log Files
•
Tune Files and Calibration Files
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6-1
Reference Information
Log Files
Log Files
Log files (*.log) are created for an Exactive instrument. The default
directory for the log files is C:\Xcalibur\system\Exactive\log. The
Instrument Configuration window shows the actual path.
Additional log files are created every time the Exactive window service
starts. The file name shows date and time of the service start, as shown
in the following example:
Thermo Exactive--2008-10-22--08-17-22.log
Each line in a log file is a message. A message has several properties that
are listed at the beginning of the line, followed by the message body.
Properties are enclosed in brackets. A property is a property name
followed by an equal sign followed by the property value. These
properties exist:
Abbreviation
Meaning
Time
Time of the message. The current local time is displayed
followed by the time offset to UTC.
Acc
Windows account name that caused this message;
“(none)” is used for an instrument source. Other known
values are “ExactiveUser” and “Xcalibur_System”.
User
User name description of the Windows account
Comp
Computer name on which this message was caused,
“(none)” is used for an instrument source.
App
Application name that caused this message; “(none)” is
used for an instrument source.
PID
Process identifier of the application process
Inst
Instrument affected
Conn
Connection in charge for the communication with the
instrument
Type
Type of the message. Message types are “info”,
“warning”, “error” and “FATAL error”
Access to the log files is regulated by the Microsoft Windows user
account or group account. Full access to the log files is granted to
Administrators. Members of the Power User group can read, delete, and
modify these files. Standard users can read these files.
6-2
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Reference Information
Tune Files and Calibration Files
Tune Files and Calibration Files
Tune files and calibration files contain information for operating the
instrument.
Tune Files
Tuning optimizes voltage settings for API source and ion transfer optics
to ensure highest sensitivity. The resulting tune file (*.mstune) is specific
to a particular analyte and solvent flow rate.
During installation of the instrument, the service engineer creates a tune
file ESI_Installation.mstune in the folder C:\Xcalibur\methods\. Use this
file as a starting point for optimizing the mass spectrometer for your
specific measurement requirements. Use this folder to store your
personal tune files.
Note Do not overwrite the default tune file
C:\Xcalibur\methods\ESI_Installation.mstune! ▲
Calibration File
After having tuned the Exactive mass spectrometer, calibrate the
instrument to ensure the mass accuracy of the measurement results.
Calibration parameters are instrument parameters whose values do not
vary with the type of experiment. They are stored AUTOMATICALLY
in a calibration file (*.mscal) in the folder
C:\Xcalibur\system\Exactive\instrument\msx_instrument_files\.
The file master_cal.mscal contained in this folder is the calibration file
used for operating the instrument. It will be overwritten with new
calibration values every time a calibration procedure is successful.
Caution Never save or change files in the folder
C:\Xcalibur\system\Exactive\instrument\msx_instrument_files\! Files in
this folder are automatically managed by the instrument software. ▲
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Reference Information
Tune Files and Calibration Files
6-4
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Glossary
This section lists and defines terms used in this manual. It also includes acronyms, metric prefixes, symbols, and
abbreviations.
A
B
C
D
E
F
G
H
I
J
K
L
A
A ampere
AC alternating current
ADC analog-to-digital converter; a device that converts
data from analog to digital form.
adduct ion An ion formed by the joining together of
two species, usually an ion and a molecule, and often
within the ion source, to form an ion containing all
the constituent atoms of both species.
AGC™ See Automatic Gain Control™ (AGC).
APCI See atmospheric pressure chemical ionization
(APCI).
APCI corona discharge current The ion current
carried by the charged particles in the APCI source.
The voltage on the APCI corona discharge needle
supplies the potential required to ionize the particles.
The APCI corona discharge current is set; the APCI
corona discharge voltage varies, as required, to
maintain the set discharge current.
See also corona discharge and APCI corona discharge
voltage.
APCI corona discharge voltage The high voltage that
is applied to the corona discharge needle in the APCI
source to produce the APCI corona discharge. The
corona discharge voltage varies, as required, to
maintain the set APCI spray current.
See also APCI spray current.
APCI manifold The manifold that houses the APCI
sample tube and nozzle, and contains the plumbing
for the sheath and auxiliary gas.
Thermo Fisher Scientific
M N
O
P
Q
R
S
T
U
V W X
Y
Z
APCI needle, corona discharge A needle to which a
sufficiently high voltage (typically ±3 to ±5 kV) is
applied to produce a chemical ionization plasma by
the corona discharge mechanism.
See also chemical ionization (CI), chemical ionization
(CI) plasma, atmospheric pressure chemical ionization
(APCI), and corona discharge.
APCI nozzle The nozzle in the APCI probe that sprays
the sample solution into a fine mist.
See also atmospheric pressure chemical ionization
(APCI).
APCI sample tube A fused silica tube that delivers
sample solution to the APCI nozzle. The APCI
sample tube extends from the sample inlet to the
APCI nozzle.
See also atmospheric pressure chemical ionization
(APCI), and API stack.
APCI source Contains the APCI probe assembly,
APCI manifold, and API stack.
See also atmospheric pressure chemical ionization
(APCI), APCI manifold, and API stack.
APCI spray current The ion current carried by the
charged particles in the APCI source. The APCI
corona discharge voltage varies, as required, to
maintain the set spray current.
APCI vaporizer A heated tube that vaporizes the
sample solution as the solution exits the sample tube
and enters the atmospheric pressure region of the
APCI source.
See also atmospheric pressure chemical ionization
(APCI).
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G-1
Glossary: API–atmospheric pressure chemical ionization (APCI)
API See atmospheric pressure ionization (API).
API atmospheric pressure region The first of two
chambers in the API source. Also referred to as the
spray chamber.
API capillary-skimmer region The area between the
capillary and the skimmer, which is surrounded by the
tube lens. It is also the area of first-stage evacuation in
the API source.
API heated capillary A tube assembly that assists in
desolvating ions that are produced by the ESI or
APCI probe.
See also API heated capillary voltage.
API heated capillary voltage The DC voltage applied
to the heated capillary. The voltage is positive for
positive ions and negative for negative ions.
See also API source and API heated capillary.
API ion transfer capillary A tube assembly that assists
in desolvating ions that are produced by the ESI, NSI,
or APCI probe.
See also API ion transfer capillary offset voltage and
API ion transfer capillary temperature.
API ion transfer capillary offset voltage A DC voltage
applied to the ion transfer capillary. The voltage is
positive for positive ions and negative for negative
ions.
See also API source and API ion transfer capillary.
API ion transfer capillary temperature The
temperature of the ion transfer capillary, which should
be adjusted for different flow rates.
See also API source and API ion transfer capillary.
API source The sample interface between the LC and
the mass spectrometer. It consists of the API probe
(ESI or APCI) and API stack.
See also atmospheric pressure ionization (API), ESI
source, APCI source, ESI probe, and API stack.
API spray chamber The first of two chambers in the
API source. In this chamber the sample liquid exits
the probe and is sprayed into a fine mist (ESI or NSI)
or is vaporized (APCI) as it is transported to the
entrance end of the ion transfer capillary.
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API spray shield A stainless steel, cylindrical vessel
that, in combination with the ESI or APCI flange,
forms the atmospheric pressure region of the
API source.
See also atmospheric pressure ionization (API).
API stack Consists of the components of the
API source that are held under vacuum and includes
the API spray shield, API ion transfer capillary,
API tube lens, skimmer, the ion transfer capillary
mount, and the tube lens and skimmer mount.
See also atmospheric pressure ionization (API) and
API source.
API tube lens A lens in the API source that separates
ions from neutral particles as they leave the ion
transfer capillary. A potential applied to the tube lens
focuses the ions toward the opening of the skimmer
and helps to dissociate adduct ions.
See also API tube lens offset voltage, API source,
API ion transfer capillary, and adduct ion.
API tube lens and skimmer mount A mount that
attaches to the heated capillary mount. The tube lens
and skimmer attach to the tube lens and skimmer
mount.
API tube lens offset voltage A DC voltage applied to
the tube lens. The value is normally tuned for a
specific compound.
See also API tube lens, adduct ion, and source CID.
AP-MALDI See atmospheric pressure matrix-assisted
laser desorption/ionization (AP-MALDI).
APPI See Atmospheric Pressure Photoionization
(APPI).
ASCII American Standard Code for Information
Interchange
atmospheric pressure chemical ionization (APCI) A
soft ionization technique done in an ion source
operating at atmospheric pressure. Electrons from a
corona discharge initiate the process by ionizing the
mobile phase vapor molecules. A reagent gas forms,
which efficiently produces positive and negative ions
of the analyte through a complex series of chemical
reactions.
See also electrospray ionization (ESI).
Thermo Fisher Scientific
Glossary: atmospheric pressure ionization (API)–consecutive reaction monitoring (CRM) scan type
atmospheric pressure ionization (API) Ionization
performed at atmospheric pressure by using
atmospheric pressure chemical ionization (APCI),
electrospray ionization (ESI), or nanospray ionization
(NSI).
B
atmospheric pressure matrix-assisted laser
desorption/ionization (AP-MALDI) Matrix-assisted
laser desorption/ionization in which the sample target
is at atmospheric pressure.
baud rate data transmission speed in events per second
See also matrix-assisted laser desorption/ionization
(MALDI).
Atmospheric Pressure Photoionization (APPI) A soft
ionization technique in which an ion is generated
from a molecule when it interacts with a photon from
a light source.
atomic mass unit Atomic Mass Unit (u) defined by
taking the mass of one atom of carbon12 as being
12u; unit of mass for expressing masses of atoms or
molecules.
Automatic Gain Control™ (AGC) Sets the ion
injection time to maintain the optimum quantity of
ions for each scan. With AGC on, the scan function
consists of a prescan and an analytical scan.
See also ion injection time.
auxiliary gas The outer-coaxial gas (nitrogen) that
assists the sheath (inner-coaxial) gas in dispersing
and/or evaporating sample solution as the sample
solution exits the APCI, ESI, or H-ESI nozzle.
auxiliary gas flow rate The relative rate of flow of
auxiliary gas (nitrogen) into the API source reported
in arbitrary units.
auxiliary gas inlet An inlet in the API probe where
auxiliary gas is introduced into the probe.
See also auxiliary gas and atmospheric pressure
ionization (API).
auxiliary gas plumbing The gas plumbing that delivers
outer coaxial nitrogen gas to the ESI or APCI nozzle.
auxiliary gas valve A valve that controls the flow of
auxiliary gas into the API source.
Thermo Fisher Scientific
b bit
B byte (8 b)
BTU British thermal unit, a unit of energy
C
°C degrees Celsius
CE central electrode (of the Orbitrap analyzer);
European conformity. Mandatory European marking
for certain product groups to indicate conformity with
essential health and safety requirements set out in
European Directives.
cfm cubic feet per minute
chemical ionization (CI) The formation of new
ionized species when gaseous molecules interact with
ions. The process can involve transfer of an electron,
proton, or other charged species between the
reactants.
chemical ionization (CI) plasma The collection of
ions, electrons, and neutral species formed in the ion
source during chemical ionization.
See also chemical ionization (CI).
CI See chemical ionization (CI).
CID See collision-induced dissociation (CID).
cm centimeter
cm3 cubic centimeter
collision gas A neutral gas used to undergo collisions
with ions.
collision-induced dissociation (CID) An ion/neutral
process in which an ion is dissociated as a result of
interaction with a neutral target species.
consecutive reaction monitoring (CRM) scan type A
scan type with three or more stages of mass analysis
and in which a particular multi-step reaction path is
monitored.
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G-3
Glossary: Convectron™ gauge–ESI flange
Convectron™ gauge A thermocouple bridge gauge that
is sensitive to the pressure as well as the thermal
conductivity of the gas used to measure pressures
between X and Y.
corona discharge In the APCI source, an electrical
discharge in the region around the corona discharge
needle that ionizes gas molecules to form a chemical
ionization (CI) plasma, which contains CI reagent
ions.
See also chemical ionization (CI) plasma and
atmospheric pressure chemical ionization (APCI).
CPU central processing unit (of a computer)
CRM See consecutive reaction monitoring (CRM) scan
type.
C-Trap curved linear trap
<Ctrl> control key on the terminal keyboard
D
d depth
Da dalton
DAC digital-to-analog converter
damping gas Helium gas introduced into the ion trap
mass analyzer that slows the motion of ions entering
the mass analyzer so that the ions can be trapped by
the RF voltage fields in the mass analyzer.
data-dependent scan A scan mode that uses specified
criteria to select one or more ions of interest on which
to perform subsequent scans, such as MS/MS or
ZoomScan.
DC direct current
divert/inject valve A valve on the mass spectrometer
that can be plumbed as a divert valve or as a loop
injector.
DS data system
DSP digital signal processor
E
EI electron ionization
electron capture dissociation (ECD) A method of
fragmenting gas phase ions for tandem mass
spectrometric analysis. ECD involves the direct
introduction of low energy electrons to trapped gas
phase ions.
See also electron transfer dissociation (ETD) and
infrared multiphoton dissociation (IRMPD).
electron multiplier A device used for current
amplification through the secondary emission of
electrons. Electron multipliers can have a discrete
dynode or a continuous dynode.
electron transfer dissociation (ETD) A method of
fragmenting peptides and proteins. In electron
transfer dissociation (ETD), singly charged reagent
anions transfer an electron to multiply protonated
peptides within the ion trap mass analyzer. This leads
to a rich ladder of sequence ions derived from cleavage
at the amide groups along the peptide backbone.
Amino acid side chains and important modifications
such as phosphorylation are left intact.
See also fluoranthene.
electrospray ionization (ESI) A type of atmospheric
pressure ionization that is currently the softest
ionization technique available to transform ions in
solution into ions in the gas phase.
EMBL European Molecular Biology Laboratory
<Enter> Enter key on the terminal keyboard
ESD ElectroStatic Discharge. Discharge of stored static
electricity that can damage electronic equipment and
impair electrical circuitry, resulting in complete or
intermittent failures.
ESI See electrospray ionization (ESI).
ESI flange A flange that holds the ESI probe in
position next to the entrance of the heated capillary,
which is part of the API stack. The ESI flange also
seals the atmospheric pressure region of the API
source and, when it is in the engaged position against
the spray shield, compresses the high-voltage
safety-interlock switch.
ECD See electron capture dissociation (ECD).
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Glossary: ESI probe–FWHM
ESI probe A probe that produces charged aerosol
droplets that contain sample ions. The ESI probe is
typically operated at liquid flows of 1 μL/min to
1 mL/min without splitting. The ESI probe includes
the ESI manifold, sample tube, nozzle, and needle.
Fast Fourier Transform (FFT) An algorithm that
performs a Fourier transformation on data. A Fourier
transform is the set of mathematical formulae by
which a time function is converted into a
frequency-domain function and the converse.
ESI source Contains the ESI probe and the API stack.
FFT See Fast Fourier Transform (FFT).
See also electrospray ionization (ESI), ESI probe, and
API stack.
fluoranthene A reagent anion that is used in an
electron transfer dissociation (ETD) experiment.
ESI spray current The flow of charged particles in the
ESI source. The voltage on the ESI spray needle
supplies the potential required to ionize the particles.
firmware Software routines stored in read-only
memory. Startup routines and low-level input/output
instructions are stored in firmware.
ESI spray voltage The high voltage that is applied to
the spray needle in the ESI source to produce the
ESI spray current. In ESI, the voltage is applied to the
spray liquid as it emerges from the nozzle.
forepump The pump that evacuates the foreline. A
rotary-vane pump is a type of forepump.
See also ESI spray current.
ETD See electron transfer dissociation (ETD).
eV Electron Volt. The energy gained by an electron that
accelerates through a potential difference of one volt.
Extensible Markup Language See XML (Extensible
Markup Language).
external lock mass A lock that is analyzed in a separate
MS experiment from your sample. If you need to run
a large number of samples, or if accurate mass samples
will be intermingled with standard samples, you might
want to use external lock masses. These allow more
rapid data acquisition by eliminating the need to scan
lock masses during each scan.
See also internal lock mass.
Fourier Transform - Ion Cyclotron Resonance Mass
Spectrometry (FT-ICR MS) A technique that
determines the mass-to-charge ratio of an ion by
measuring its cyclotron frequency in a strong
magnetic field.
fragment ion A charged dissociation product of an
ionic fragmentation. Such an ion can dissociate
further to form other charged molecular or atomic
species of successively lower formula weights.
fragmentation The dissociation of a molecule or ion to
form fragments, either ionic or neutral. When a
molecule or ion interacts with a particle (electron, ion,
or neutral species) the molecule or ion absorbs energy
and can subsequently fall apart into a series of charged
or neutral fragments. The mass spectrum of the
fragment ions is unique for the molecule or ion.
FT Fourier Transformation
F
FT-ICR MS See Fourier Transform - Ion Cyclotron
Resonance Mass Spectrometry (FT-ICR MS).
f femto (10-15)
FTMS Fourier Transformation Mass Spectrometry
°F degrees Fahrenheit
full-scan type Provides a full mass spectrum of each
analyte or parent ion. With the full-scan type, the
mass analyzer is scanned from the first mass to the last
mass without interruption. Also known as single-stage
full-scan type.
.fasta file extension of a SEQUEST™ search database
file
ft foot
FWHM Full Width at Half Maximum
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G-5
Glossary: g–ion optics
G
Hz hertz (cycles per second)
g gram
I
G Gauss; giga (109)
ICR ion cyclotron resonance
GC gas chromatograph; gas chromatography
ID inside diameter
GC/MS gas chromatography / mass spectrometer
IEC International Electrotechnical Commission
GUI graphical user interface
IEEE Institute of Electrical and Electronics Engineers
H
in. inch
h hour
infrared multiphoton dissociation (IRMPD) In
infrared multiphoton dissociation (IRMPD), multiply
charged ions consecutively absorb photons emitted by
a infrared laser until the vibrational excitation is
sufficient for their fragmentation. The fragments
continue to pick up energy from the laser pulse and
fall apart further to ions of lower mass.
h height
handshake A signal that acknowledges that
communication can take place.
HCD See higher energy collision-induced dissociation
(HCD).
header information Data stored in each data file that
summarizes the information contained in the file.
H-ESI probe Heated-electrospray ionization (H-ESI)
converts ions in solution into ions in the gas phase by
using electrospray ionization (ESI) in combination
with heated auxiliary gas.
higher energy collision-induced dissociation (HCD)
Collision-induced dissociation that occurs in the
HCD cell of the Orbitrap mass analyzer. The
HCD cell consists of a straight multipole mounted
inside a collision gas-filled tube. A voltage offset
between C-Trap and HCD cell accelerates parent ions
into the collision gas inside the HCD cell, which
causes the ions to fragment into product ions. The
product ions are then returned to the Orbitrap
analyzer for mass analysis. HCD produces triple
quadrupole-like product ion mass spectra.
high performance liquid chromatography (HPLC)
Liquid chromatography in which the liquid is driven
through the column at high pressure. Also known as
high pressure liquid chromatography.
HPLC See high performance liquid chromatography
(HPLC).
See also electron capture dissociation (ECD).
instrument method A set of experiment parameters
that define Xcalibur operating settings for the
autosampler, liquid chromatograph (LC), mass
spectrometer, divert valve, syringe pump, and so on.
Instrument methods are saved as file type .meth.
internal lock mass A lock that is analyzed during the
same MS experiment as your sample and is contained
within the sample solution or infused into the
LC flow during the experiment. Internal lock masses
provide the most accurate corrections to the data.
See also external lock mass.
I/O input/output
ion gauge Measures the pressure in the mass analyzer
region (high vacuum region) of the vacuum manifold.
ion injection time The amount of time that ions are
allowed to accumulate in the ion trap mass analyzer
when AGC is off. With AGC on, the ion injection
time is set automatically (up to the set maximum ion
injection time) based on the AGC target value.
See also: Automatic Gain Control™ (AGC).
ion optics Focuses and transmits ions from the
API source to the mass analyzer.
HV high voltage
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Thermo Fisher Scientific
Glossary: ion source–MH+
ion source A device that converts samples to gas-phase
ions.
ion sweep cone A removable cone-shaped metal cover
that fits on top of the API ion transfer capillary and
acts as a physical barrier to protect the entrance of the
capillary.
ion sweep gas Extra nitrogen gas that flows along the
axis of the API ion transfer capillary (between the ion
sweep cone and the capillary block) towards the API
spray. The sweep gas flow is thus countercurrent to the
flow of the ions.
See also ion sweep gas pressure.
ion sweep gas pressure The rate of flow of the sweep
gas (nitrogen) into the API source. A measurement of
the relative flow rate (in arbitrary units) to provide the
required flow of nitrogen gas out from the Ion Sweep
cone towards the API spray.
See also ion sweep gas.
LED light-emitting diode
LHe liquid helium
liquid chromatography (LC) A form of elution
chromatography in which a sample partitions between
a stationary phase of large surface area and a liquid
mobile phase that percolates over the stationary phase.
liquid chromatography / mass spectrometry
(LC/MS) An analytical technique in which a
high-performance liquid chromatograph (LC) and a
mass spectrometer (MS) are combined.
LN2 liquid nitrogen
lock mass A known reference mass in the sample that is
used to correct the mass spectral data in an accurate
mass experiment and used to perform a real-time
secondary mass calibration that corrects the masses of
other peaks in a scan. Lock masses with well-defined,
symmetrical peaks work best. You can choose to use
internal lock mass or external lock mass.
IRMPD See infrared multiphoton dissociation
(IRMPD).
log file A text file, with a .log file extension, that is used
to store lists of information.
K
M
k kilo (103, 1000)
μ micro (10-6)
K kilo (210, 1024)
m meter; milli (10-3)
KEGG Kyoto Encyclopedia of Genes and Genomes
M mega (106)
kg kilogram
M+ molecular ion
L
MALDI See matrix-assisted laser desorption/ionization
(MALDI).
l length
L liter
LAN local area network
lb pound
LC See liquid chromatography (LC).
LC/MS See liquid chromatography / mass spectrometry
(LC/MS).
matrix-assisted laser desorption/ionization
(MALDI) A method of ionizing proteins where a direct
laser beam is used to facilitate vaporization and
ionization while a matrix protects the biomolecule
from being destroyed by the laser.
See also atmospheric pressure matrix-assisted laser
desorption/ionization (AP-MALDI).
MB Megabyte (1048576 bytes)
MH+ protonated molecular ion
Thermo Fisher Scientific
Exactive Software Manual (P/N 1249910, Revision C)
G-7
Glossary: microscan–Orbitrap mass analyzer
microscan One mass analysis (ion injection and storage
or scan-out of ions) followed by ion detection.
Microscans are summed, to produce one scan, to
improve the signal-to-noise ratio of the mass spectral
data. The number of microscans per scan is an
important factor in determining the overall scan time.
min minute
mL milliliter
mm millimeter
MRFA A peptide with the amino acid sequence
methionine–arginine–phenylalanine–alanine.
MS mass spectrometer; mass spectrometry
MS MSn power: where n = 1
MS scan modes Scan modes in which only one stage of
mass analysis is performed. The scan types used with
the MS scan modes are full-scan type and selected ion
monitoring (SIM) scan type.
MSDS Material Safety Data Sheet
MS/MS Mass spectrometry/mass spectrometry, or
tandem mass spectrometry is an analytical technique
that involves two stages of mass analysis. In the first
stage, ions formed in the ion source are analyzed by an
initial analyzer. In the second stage, the mass-selected
ions are fragmented and the resultant ionic fragments
are mass analyzed.
MSn scan mode The scan power equal to 1 to 10,
where the scan power is the power n in the expression
MSn. MSn is the most general expression for the scan
mode, which can include the following:
• The scan mode corresponding to the one stage of
mass analysis in a single-stage full-scan experiment
or a selected ion monitoring (SIM) experiment
• The scan mode corresponding to the two stages of
mass analysis in a two-stage full-scan experiment or
a selected reaction monitoring (SRM) experiment
• The scan mode corresponding to the three to ten
stages of mass analysis (n = 3 to n = 10) in a
multi-stage full-scan experiment or a consecutive
reaction monitoring (CRM) experiment
G-8
Exactive Software Manual (P/N 1249910, Revision C)
See also MS scan modes and MS/MS.
multipole A symmetrical, parallel array of (usually)
four, six, or eight cylindrical rods that acts as an ion
transmission device. An RF voltage and DC offset
voltage are applied to the rods to create an electrostatic
field that efficiently transmits ions along the axis of
the multipole rods.
m/z Mass-to-charge ratio. An abbreviation used to
denote the quantity formed by dividing the mass of an
ion (in u) by the number of charges carried by the ion.
For example, for the ion C7H72+, m/z=45.5.
N
n nano (10-9)
nanospray ionization (NSI) A type of electrospray
ionization (ESI) that accommodates very low flow
rates of sample and solvent on the order of 1 to
20 nL/min (for static nanospray) or 100
to 1000 nL/min (for dynamic nanospray).
NCBI National Center for Biotechnology Information
(USA)
NIST National Institute of Standards and Technology
(USA)
NMR Normal Mass Range
NSI See nanospray ionization (NSI).
O
octapole An octagonal array of cylindrical rods that acts
as an ion transmission device. An RF voltage and
DC offset voltage applied to the rods create an
electrostatic field that transmits the ions along the axis
of the octapole rods.
OD outside diameter
Orbitrap mass analyzer The Orbitrap™ mass analyzer
consists of a spindle-shape central electrode
surrounded by a pair of bell-shaped outer electrodes.
Ions inside the mass analyzer orbit in stable
trajectories around the central electrode with
harmonic oscillations along it.
Thermo Fisher Scientific
Glossary: OT–raw data
P/N part number
r
p-p peak-to-peak voltage
z
ppm parts per million
Two detection electrodes record an image current of
the ions as they undergo harmonic oscillations. A
Fourier transformation extracts different harmonic
frequencies from the image current. An ion's
mass-to-charge ratio m/z is related to the frequency f
of its harmonic oscillations and to the instrumental
constant k by:
m/z = k/f 2
OT Orbitrap
See Orbitrap mass analyzer.
PQD pulsed-Q dissociation
precursor ion An electrically charged molecular species
that can dissociate to form fragments. The fragments
can be electrically charged or neutral species. A
precursor ion (PR) can be a molecular ion or an
electrically charged fragment of a molecular ion. Also
known as parent ion.
precursor mass Mass of the corresponding precursor
(or parent) ion or molecule.
psig pounds per square inch, gauge
OVC outer vacuum case
PTM posttranslational modification
Ω ohm
pulsed Q dissociation (PQD) Collision-induced
dissociation that involves precursor ion activation at
high Q, a time delay to allow the precursor to
fragment, and then a rapid pulse to low Q where all
fragment ions are trapped. The fragment ions can
then be scanned out of the ion trap mass analyzer and
detected. PQD eliminates the “1/3 Rule” low mass
cut-off for MS/MS data.
P
p pico (10-12)
Pa pascal
parent ion An electrically charged molecular species
that can dissociate to form fragments. The fragments
can be electrically charged or neutral species. A parent
ion can be a molecular ion or an electrically charged
fragment of a molecular ion. Also called a precursor
ion.
parent mass The mass-to-charge ratio of a parent ion.
The location of the center of a target parent-ion peak
in mass-to-charge ratio (m/z) units. Also known as
precursor mass.
See also parent ion.
PCB printed circuit board
PDA detector Photodiode Array detector is a linear
array of discrete photodiodes on an integrated circuit
chip. It is placed at the image plane of a spectrometer
to allow a range of wavelengths to be detected
simultaneously.
PE protective earth
PID proportional / integral / differential
Thermo Fisher Scientific
Q
quadrupole A symmetrical, parallel array of four
hyperbolic rods that acts as a mass analyzer or an ion
transmission device. As a mass analyzer, one pair of
opposing rods has an oscillating radio frequency (RF)
voltage superimposed on a positive direct current
(DC) voltage. The other pair has a negative DC
voltage and an RF voltage that is 180 degrees out of
phase with the first pair of rods. This creates an
electrical field (the quadrupole field) that efficiently
transmits ions of selected mass-to-charge ratios along
the axis of the quadrupole rods.
R
RAM random access memory
raw data Uncorrected liquid chromatograph and mass
spectrometer data obtained during an acquisition.
Xcalibur and Xcalibur-based software store this data in
a file that has a .raw file extension.
Exactive Software Manual (P/N 1249910, Revision C)
G-9
Glossary: resolution–sheath gas valve
resolution The ability to distinguish between two
points on the wavelength or mass axis.
retention time (RT) The time after injection at which
a compound elutes. The total time that the compound
is retained on the chromatograph column.
RF radio frequency
RF lens A multipole rod assembly that is operated with
only radio frequency (RF) voltage on the rods. In this
type of device, virtually all ions have stable trajectories
and pass through the assembly.
RF voltage An AC voltage of constant frequency and
variable amplitude that is applied to the ring electrode
or endcaps of the mass analyzer or to the rods of a
multipole. Because the frequency of this AC voltage is
in the radio frequency (RF) range, it is referred to as
RF voltage.
RMS root mean square
ROM read-only memory
rotary-vane pump A mechanical vacuum pump that
establishes the vacuum necessary for the proper
operation of the turbomolecular pump. (Also called a
roughing pump or forepump.)
RS-232 An accepted industry standard for serial
communication connections. This Recommended
Standard (RS) defines the specific lines and signal
characteristics used by serial communications
controllers to standardize the transmission of serial
data between devices.
RT An abbreviated form of the phrase retention time
(RT). This shortened form is used to save space when
the retention time (in minutes) is displayed in a
header, for example, RT: 0.00-3.75.
S
s second
scan mode and scan type combinations A function
that coordinates the three processes in the
MS detector: ionization, mass analysis, and ion
detection. You can combine the various scan modes
and scan types to perform a wide variety of
experiments.
G-10
Exactive Software Manual (P/N 1249910, Revision C)
selected ion monitoring (SIM) scan type A scan type
in which the mass spectrometer acquires and records
ion current at only one or a few selected
mass-to-charge ratio values.
See also selected reaction monitoring (SRM) scan
type.
selected reaction monitoring (SRM) scan type A scan
type with two stages of mass analysis and in which a
particular reaction or set of reactions, such as the
fragmentation of an ion or the loss of a neutral moiety,
is monitored. In SRM a limited number of product
ions is monitored.
SEM secondary electron multiplier
Serial Peripheral Interface (SPI) hardware and
firmware communications protocol
serial port An input/output location (channel) for
serial data transmission.
sheath gas The inner coaxial gas (nitrogen), which is
used in the API source to help nebulize the sample
solution into a fine mist as the sample solution exits
the ESI or APCI nozzle.
sheath gas flow rate The rate of flow of sheath gas into
the API source. A measurement of the relative flow
rate (in arbitrary units) that needs to be provided at
the sheath gas inlet to provide the required flow of
sheath gas to the ESI or APCI nozzle.
sheath gas inlet An inlet in the API probe where sheath
gas is introduced into the probe.
sheath gas plumbing The gas plumbing that delivers
sheath gas to the ESI or APCI nozzle.
sheath gas pressure The rate of flow of sheath gas
(nitrogen) into the API source. A measurement of the
relative flow rate (in arbitrary units) that needs to be
provided at the sheath gas inlet to provide the required
flow of inner coaxial nitrogen gas to the ESI or APCI
nozzle. A software-controlled proportional valve
regulates the flow rate.
See also sheath gas.
sheath gas valve A valve that controls the flow of
sheath gas into the API source. The sheath gas valve is
controlled by the data system.
Thermo Fisher Scientific
Glossary: signal-to-noise ratio (S/N)–V DC
signal-to-noise ratio (S/N) The ratio of the signal
height (S) to the noise height (N). The signal height is
the baseline corrected peak height. The noise height is
the peak-to-peak height of the baseline noise.
SIM See selected ion monitoring (SIM) scan type.
skimmer A vacuum baffle between the higher pressure
capillary-skimmer region and the lower pressure
region. The aperture of the skimmer is offset with
respect to the bore of the ion transfer capillary.
source CID A technique for fragmenting ions in an
atmospheric pressure ionization (API) source.
Collisions occur between the ion and the background
gas, which increase the internal energy of the ion and
stimulate its dissociation.
SPI See Serial Peripheral Interface (SPI).
SRM See selected reaction monitoring (SRM) scan
type.
sweep gas Nitrogen gas that flows out from behind the
sweep cone in the API source. Sweep gas aids in
solvent declustering and adduct reduction.
See also sweep gas flow rate.
sweep gas flow rate The rate of flow of sweep gas into
the API source. A measurement of the relative flow
rate (in arbitrary units) to provide the required flow of
nitrogen gas to the sweep cone of the API source.
See also sweep gas.
syringe pump A device that delivers a solution from a
syringe at a specified rate.
T
T Tesla
total ion current (TIC) The sum of the ion current
intensities across the scan range in a mass spectrum.
tube lens offset The voltage offset from ground that is
applied to the tube lens to focus ions toward the
opening of the skimmer.
See also source CID.
Tune Method A defined set of mass spectrometer tune
parameters for the ion source and mass analyzer. Tune
methods are defined by using the instrument
software’s tune window and saved as tune file.
A tune method stores tune parameters only.
(Calibration parameters are stored separately, not with
the tune method.)
tune parameters Instrument parameters whose values
vary with the type of experiment.
turbomolecular pump A vacuum pump that provides
a high vacuum for the mass spectrometer and detector
system.
TWA time weighted average
U
u atomic mass unit
UHV ultra high vacuum
ultra-high performance liquid chromatography
(U-HPLC) See high performance liquid
chromatography (HPLC).
Ultramark 1621 A mixture of
perfluoroalkoxycyclotriphosphazenes used for ion trap
calibration and tuning. It provides ESI singly charged
peaks at m/z 1022.0, 1122.0, 1222.0, 1322.0, 1422.0,
1522.0, 1622.0, 1722.0, 1822.0, and 1921.9.
target compound A compound that you want to
identify or quantitate or that a specific protocol (for
example, an EPA method) requires that you look for.
Target compounds are also called analytes, or target
analytes.
UMR Universal Mass Range
TIC See total ion current (TIC).
V AC volts alternating current
TMP See turbomolecular pump.
V DC volts direct current
V
V volt
Torr A unit of pressure, equal to 1 mm of mercury and
133.32 Pa.
Thermo Fisher Scientific
Exactive Software Manual (P/N 1249910, Revision C)
G-11
Glossary: vacuum manifold–XML (Extensible Markup Language)
vacuum manifold A thick-walled, aluminum chamber
with machined flanges on the front and sides and
various electrical feedthroughs and gas inlets that
encloses the API stack, ion optics, mass analyzer, and
ion detection system.
W
vacuum system Components associated with lowering
the pressure within the mass spectrometer. A vacuum
system includes the vacuum manifold, pumps,
pressure gauges, and associated electronics.
WEEE European Union Waste Electrical and
Electronic Equipment Directive. Provides guidelines
for disposal of electronic waste.
vent valve A valve that allows the vacuum manifold to
be vented to air or other gases. A solenoid-operated
valve.
vol volume
G-12
Exactive Software Manual (P/N 1249910, Revision C)
w width
W watt
X
XML (Extensible Markup Language) A
general-purpose markup language that is used to
facilitate the sharing of data across different
information systems, particularly via the Internet.
Thermo Fisher Scientific
Index
Symbols
.csv file 3-19–3-20, 4-73, 4-75, 5-4
.log file 6-2
.meth file 4-39
.mscal file 6-3
.mstune file 3-10, 4-5, 4-8, 6-3
.raw file 4-38
.txt file 3-19–3-20, 4-73, 4-75, 5-4
.xml file 3-19–3-20, 4-70, 4-73, 4-75, 5-4
A
About dialog box 1-2, 4-62
acquisition time 3-8–3-9, 4-40
Acquisition window 4-38
AGC target value 3-13, 4-14
analysis graphs window
description 4-56
shortcut menu 4-58
toolbar 4-57
zooming 4-57
APCI
capillary temperature 4-30
capillary voltage 4-31
corona discharge current 4-30
corona discharge voltage 4-30
sheath gas flow rate 4-29
skimmer voltage 4-31
source 4-28
source window 4-28
sweep gas flow rate 4-29
tube lens voltage 4-31
vaporizer temperature 4-32
APPI
sheath gas flow rate 4-33
skimmer voltage 4-36
source 4-33
source discharge current 4-35
source discharge voltage 4-34
source heated capillary temperature 4-35
source heated capillary voltage 4-36
source lamp 3-17
source tube lens voltage 4-36
source vaporizer temperature 4-37
source window 4-32
sweep gas flow rate 4-34
asterisk, in the title bar 4-3
audit information 3-4, 3-6
Thermo Fisher Scientific
autosampler 4-40
auxiliary gas
APCI 4-29
APPI 4-34
ESI 4-16
H-ESI 4-20
NSI 4-25
B
bakeout
duration 4-48
procedure 5-13
C
Calibrate window 4-44
calibration file 6-3
calibration parameters 4-44
calibration solution 4-44, 4-46, 5-18
capillary
temperature 4-17, 4-21, 4-26
voltage 4-18, 4-27
center mass 3-15, 4-67
CID 4-42
collision energy 3-16, 4-68
clipboard 3-19–3-20, 4-55, 4-62, 4-73
comma separated values text file 5-4
comment, on current sample 4-39
communication status 2-2, 4-9
connection status 1-2
contact closure 3-28, 4-40–4-41
cooling and stabilization time 4-48
creep mode 4-53
D
data acquisition 4-41
debug messages window 4-58
dialog boxes 4-61
Display Options dialog box 4-78
display panel 4-4
Divert Valves page 3-25
duration
of bakeout 4-48
of segments 3-11
of switch events 3-26
Exactive Software Manual (P/N 1249910, Revision C) I-1
Index: E–L
E
elapsed time
of current acquisition 4-38
of current procedure 4-43, 4-45, 4-47, 4-49
electronics service switch 5-13
error diagnosis 4-48, 4-54
ESI
auxiliary gas flow rate 4-16
capillary voltage 4-18
sheath gas flow rate 4-15
skimmer voltage 4-18
source window 4-15
spray current 4-17
spray voltage 4-17
sweep gas flow rate 4-16
tube lens voltage 4-18
Evaluate window 4-46
evaluation procedure 4-46
Exactive Configuration window 1-1
Exactive Tune
version 4-62
window 4-2
Exactive window service 6-2
exporting lock masses 5-3–5-4
F
File menu 3-3
File Save - Audit Trail dialog box 3-4, 3-6
File Summary Information Dialog Box 3-6
flow rate 3-24, 4-65
forevacuum line 4-48
fragmentation
settings 3-16, 4-13, 4-68
type 4-52
Fragmentation dialog box 3-16, 4-68
H
Hamilton syringe 3-23
hardware status 2-2, 4-9
HCD 4-13
collision cell 4-42, 4-68
collision energy 3-16, 4-68
collision gas 4-68
header information 3-4, 3-6
Help menu 3-5
H-ESI
capillary voltage 4-22
heater temperature 4-23
sheath gas flow rate 4-20
skimmer voltage 4-22
source 4-19
spray current 4-21
I-2
Exactive Software Manual (P/N 1249910, Revision C)
spray voltage 4-21
sweep gas flow rate 4-20
tube lens voltage 4-22
HESI source window 4-19
high vacuum chamber 4-48, 5-15
Home Page window 2-1
Hot link 4-12, 4-14
I
image files 4-53, 4-58
importing lock masses 5-7
inject time 4-52
inside diameter, for syringes 4-65
in-source CID 4-13, 4-42, 4-68
instrument bakeout 4-47
Instrument Configuration program 3-2–3-3
Instrument Control panel 4-11
instrument files 1-2
instrument identification 4-62
instrument method 3-4, 3-6, 4-39, 4-52
Instrument Setup window 3-2
instrument status 1-2, 4-8
instrument status window 4-54
shortcut menus 4-54
Vacuum System node 4-48
ion polarity 3-13, 4-52
ion source region 4-48
ionization method 4-37
IP address 1-2
IP address range 1-2
L
LC 4-42
license 4-62
key 4-63
License dialog box 4-63
list, of recent scans 4-12
lock mass collection
deleting 4-76
name 4-75, 4-77
selecting 3-17
Lock Mass Replacement dialog box 4-75
lock masses
creating 3-18, 4-72
editing 4-71
exporting 5-3
usage 3-11, 4-14, 4-78
Lock Masses dialog box 4-71, 5-18
log file 1-2
logon ID 3-3
Thermo Fisher Scientific
Index: M–S
M
mains failure 5-13
manual control, of syringe pump 4-65
mass accuracy 5-21
Mass Calibration 5-21
mass resolution 3-13, 4-13, 4-78
maximum injection time 3-14, 4-14
maximum value, for scan range 3-15, 4-67
messages window 4-55
method summary 3-3
microscan 3-13, 4-13, 4-52
minimum segment time 3-8
minimum value, for scan range 3-15, 4-67
mouse
panning 4-52–4-53, 4-57
wheel 4-51, 4-57
zooming 4-53
MS Detector Setup page 3-7–3-8
power failure 5-13
precision, of mass positions 4-78
pressure values 4-47
print preview 4-52, 4-57
printer’s parameters 4-52, 4-57
printing 3-4, 3-31
pumping, the system 5-13
Q
Qual Browser 4-38
R
removing gases 5-13
Reports menu 4-6
resolution 3-13, 4-13
retention time 3-26
RS-232 5-20
N
nanospray ionization 4-24
negative ion mode, calibration 4-45
network address 1-2
network drives 4-38
New Method page 3-7
noise level 4-52
NSI
sheath gas flow rate 4-24
skimmer voltage 4-27
source 4-24
source window 4-24
spray current 4-26
spray voltage 4-26
sweep gas flow rate 4-25
tube lens voltage 4-27
number
of scan events 3-11
of scan segments 3-9
of scans 4-52
O
Orbitrap chamber 4-48
P
page setup 3-4
Pathfinder 4-41
performance status 2-2, 4-10, 5-21
Pirani gauge 4-48
polarity 3-13, 4-13
positive ion mode, calibration 4-44
Thermo Fisher Scientific
S
sample name 4-39
scan event 3-11–3-12, 4-52
Scan Parameters History dialog box 4-66
Scan Parameters window 4-12
scan range 3-14, 4-12, 4-52, 4-66
Scan range dialog box 3-14, 4-66
scan segment 3-9, 4-52
scan settings 3-12
scan type 4-52
segment duration 3-11
Sequence Setup View 4-8
setup parameters 3-2–3-3
shortcut menus
analysis graphs window 4-58
debug messages window 4-59
instrument status window 4-54
Lock Masses dialog box 3-19, 4-72
spectrum window 4-53
Status page 2-1
tray icon 4-2
skimmer 4-42
source CID 4-13, 4-42, 4-68
source type 4-52
spectrum window
display options 4-78
toolbar 4-52
visibility 4-50
zooming 4-51
standby mode 4-49
start delay 3-23
Status page, of Information view 2-1
Exactive Software Manual (P/N 1249910, Revision C)
I-3
Index: T–Z
status, of current acquisition 4-38
Summary page 3-31
switch events
duration 3-22–3-23
number 3-22
switch positions
of switching valves 3-26
of syringe pump 3-22
switches, electronics service 5-13
syringe
diameter 3-24
type 3-21, 4-64
volume 3-23, 4-64
syringe pump
interface 5-20
manual control 4-65
operating status 3-22, 4-9
parameters 4-64
system bakeout 5-13
system tray, in Microsoft Windows 4-2
Tune Method 3-10, 4-3, 4-5, 4-8
tune parameters 4-42
Tune window 4-42
tuning
availability 4-42
solution 4-42
U
Unimetrics syringe 3-23
user self-identification 3-3
V
Vacuum / Bakeout window 4-47
vacuum gauges 4-47
Vacuum System node 4-48
validity period, of mass calibration 5-21
valve position 4-9
View bar 3-3
T
tasks panel 4-3, 4-11
text editor 4-55
TIC 4-43
time delay 3-9
title bar 4-3
toggling, between mouse panning and mouse zooming 4-53
toolbars
analysis graphs window 4-57
Exactive Tune window 4-8
spectrum window 4-52
total ion current (TIC) intensity 4-43
tune default values 3-12
tune file 6-3
I-4
Exactive Software Manual (P/N 1249910, Revision C)
W
width, of scan range 3-15, 4-67
X
Xcalibur 4-8, 4-38, 4-41
Z
zooming
analysis graphs window 4-51, 4-57
spectrum window 4-51
Thermo Fisher Scientific
Thermo Fisher Scientific Inc.
81 Wyman Street
P.O. Box 9046
Waltham, Massachussetts 02454-9046
United States
www.thermo.com
Part of Thermo Fisher Scientific
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