Development of a Client Tool for a Mass Spectral

Development of a Client Tool for a Mass Spectral
ASMS2011 ThP383
Development of a client tool for a mass spectra database
Satoshi Tanaka1, Shigeki Kajihara 1, Shinichi Utsunomiya1, Tsuyoshi Tabata 2, Ken Aoshima2, Yoshiya Oda 2, Yoshito Nihei3, Takaaki Nishioka3 , Koichi Tanaka1
1 SHIMADZU CORPORATION, Nishinokyo-kuwabaracho, Nakagyo-ku, Kyoto 604-8511, Japan
2 Eisai Co., Ltd., Tokodai 5-1-3, Tsukuba, 300-2635, Japan
Commercial software attached to an MS instrument is usually used to deal with MS raw data after acquisition by a mass spectrometer. However, it has some of the following problems:
• It cannot read file formats from other mass spectrometers. So the same analysis methods might not be able to be used with different file formats.
• It must be used with a valid license. So when dealing with a huge amount of data, multiple tasks cannot be executed without extra licenses.
• It cannot be controlled by third-party software. Therefore analysis using original methods or algorithms is not easy.
To solve these problems, we have developed a new software product named Mass++.
MassBank is a public repository database of mass spectra, currently containing 30,857 data. To search the data on a large scale, users had to manually repeat extracting peak data from raw data and submitting
them to MassBank. To relieve researchers from these tedious manual tasks, we cooperated to add new functions to Mass++ and MassBank.
2: Mass++
3: MassBank [1]
Mass++ is software for viewing and manipulating mass spectra, which supports various data formats as listed below.
Software
Company
extension
Input / Output
MassBank currently contains 30,857 mass spectral data provided by twenty laboratories.
In addition, MassBank provides functions for database search via a web application. So
anyone can use them freely with a web browser such as Internet Explorer or Firefox.
LCMS solution
Shimadzu
.lcd
Input
Table 2 Database services of MassBank
GCMS solution
Shimadzu
.qgd
Input
Service
Details
Analyst, Analyst QS
Applied Biosystems
.wiff
Input
Spectrum Search
Search similar spectra on a peak-by-peak basis
Xcalibur
Thermo Fisher
.raw
Input
Quick Search
Keyword search of chemical compounds
.raw
Input
Peak Search
Search spectra by m/z values and molecular formulae
.mzXML .mzML
Input / Output
Substructure Search
Search chemical compounds by substructures
.msb
Input / Output
Advanced Search
Search similar spectra on a neutral loss-to-neutral loss basis
Spectral Browser
3D viewer of user’s spectra
Batch Service
Similarity search of MSn spectra in a batch process
Browse Page
Hierarchical browsing of all data
Record Index
Categorized list of spectra
Table 1 Supported data formats
Waters
mzXML / mzML
MSB
(Mass++ Original Format)
Mass++ is a plug-in style software application. So users can customize it depending on their purposes such as addition
of new functions and deleting unnecessary functions to increase performance, without editing Mass++ source code.
Function
Function
It is easy to add/remove.
JST and Keio University, Baba-cho 14-1, Tsuruoka, 997-0035, Japan
4: Linking Mass++ and MassBank
1: Introduction
MassLynx
3 BIRD,
Function
Mass++ is plug-in style software, so functions related to MassBank are also implemented as a plug-in. MassBank provides a SOAP (Simple Object Access Protocol) API (Application Programming Interface) as well as a
web application, which enables applications to be written without requiring a web browser. Mass++ can perform a search in MassBank through its SOAP API.
4-1: Database Search
To register MS spectra in MassBank, text files called “MassBank records” are required.
Contributors usually manually prepare MassBank records from their raw data analyzed on
various kinds of MS instruments. It was very time-consuming to extract sample information, setup parameters and peak data. Furthermore, the way of extracting them is different according to
the software. On the other hand, Mass++ can export MassBank records semi-automatically by
extracting information from raw data and detecting peaks. These records can then be easily
registered in MassBank.
Table 3 Database Search Services of MassBank supported in Mass++
Database Search
Details
Spectrum Search
Search similar spectra on a peak-by-peak basis
Peak Search
Search spectra by m/z values
Peak Difference Search
Search spectra by m/z differences
Batch Search
Search similar spectra in a batch process.
(This function will be supported in the next version of Mass++)
Using Web Browser
Raw Data
Peak List
MS Software
Web Browser
Mass++ is plug-in style all-purpose software for Mass Spectrometry.
MassBank is a powerful database for MS spectra.
Mass++ and MassBank make it easy to search similar spectra with a large query dataset.
and select a spectrum.
Mass++
-Future Plans
3. Paste into the
browser.
2. Send to MassBank.
Figure 2 Mass++ Functions
Mass++ can be freely downloaded from the web site:
http://masspp.jp/
• Higher performance/accuracy peak detection algorithm
• A more user-friendly user interface
4. Send to MassBank.
Spectrum Search
3. Get the result.
Spectral Browser
• Development of MassBank REST API
Mass++ ver. 2.0.0.
5. Get the result.
The latest version of Mass++ is 1.7.4.
We are preparing to distribute Mass++ 2.0.0.
Figure 4 Data flow in MassBank search
After searching, the search results are displayed and peaks in MassBank can be overlaid onto the waveform of
spectra displayed by Mass++ to confirm how similar they are.
Spectrum
Search Result
Differential Analysis
It will be released this September. Please check the Mass++ website.
- Reference
[1] MassBank: A public repository for sharing mass spectral data for life sciences
H.Horai, M.Arita, S.Kanaya, Y.Nihei, T.Ikeda, K.Suwa, Y.Ojima, K.Tanaka, S.Tanaka,
Overlapping
K.Aoshima, Y.Oda, Y.Kakazu, M.Kusano, T.Tohge, F.Matsuda, Y.Sawada, M.Yokota Hirai,
H.Nakanishi, K.Ikeda, N.Akimoto, T.Maoka, H.Takahashi, T.Ara, N.Sakurai, H.Suzuki,
Figure 3 Database services of MassBank
View
MassBank Record
5: Summary
1. Read the raw data
Details
3D View
ACC ESSION : GN L3WJD 3
R EC OR D_TITLE: Sam ple Spectrum (Scan=1, R T=0.0049)
D ATE: 2011.05.12
AU THORS: Satoshi Tanaka
C OPYRIGH T: SHIMADZ U C orporation
AC $INSTRU MEN T: LC-ESI-IT-TOF -MS
AC $INSTRU MEN T_TYPE: LC -ESI -IT-TOF -MS
AC $AN ALY TIC AL_C OND ITION: MS_TY PE LC/MS
AC $AN ALY TIC AL_C OND ITION: MOD E POSITIVE
AC $AN ALY TIC AL_C OND ITION: R ETEN TION_TIME 0.077788 m in
AC $C OMMEN T: Peaks C ount = 2041
AC $C OMMEN T: Max Peak Value = 433722.109375
PK$NU M_PEAK: 2041
PK$PEAK: m/z int. rel.int.
200.521958 509.538589 1
297.595126 2272.276123 5
…
Figure 6 Creating a MassBank record using Mass++
1. Read the raw data
and select a spectrum.
2. Extract
peak list.
Mass++ supports new plug-ins written in the C/C++, C++/CLI, C#.NET or VB.NET programming languages, to expand
its functionality.
Also, Mass++ has many functions implemented as plug-ins such as Profile View, 3D View, Overlapping, Peak
Detection, Smoothing, Baseline Subtraction, Background Subtraction, Data Fusion, Quantitation and so on.
Peak Detection
Profile View
Heat map View
Overlapping
Export
MassBank
Using new Mass++
MassBank
Raw Data
Function
Figure 1 plug-in
Spectrum
Previously users had to extract peak data in text format and paste it into the browser because raw data is not
accepted as a query for spectral search in MassBank. Using new Mass++, users can search MassBank data by
simply selecting a raw data spectrum for a MassBank query.
A plug-in can call
another plug-in.
Mass++
4-2: MassBank Record
Mass++ supports some database search functions of MassBank.
Contributors to MassBank provide PCs as their own data servers for publishing their data.
The MassBank system and installer for Windows and Linux is available as open source
software. Additionally the system is useful for building personal or group mass spectra
databases in the laboratory.
MassBank is available on the website:
http://www.massbank.jp/
Search
Peak List
D.Shibata, S.Neumann, T.Iida, K.Tanaka, K.Funatsu, F.Matsuura, T.Soga, R.Taguchi,
K.Saito and T.Nishioka, J.Mass Spectrom., 45, 703-714(2010)
or
m/z values
m/z differences
-Acknowledgment
This research is granted by the Japan Society for the Promotion of Science (JSPS) through
the “Funding Program for World-Leading Innovative R&D on Science and Technology
Figure 5 MassBank search results shown in Mass++
(FIRST Program), “initiated by the Council for Science and Technology Policy (CSTP).
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