质谱分析软件教程MSFinder-Tutorial.pdf

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MS-FINDER tutorial Last edited in 2015/010/19 Abstract The purpose of metabolomics is to perform the ‘comprehensive’ analysis for small biomolecules of living organisms. Liquid chromatography coupled with electrospray ionization- (ESI-) tandem mass spectrometer (LC/MS/MS) is the preferred tool for untargeted metabolomics. Currently, the main bottleneck of LC/MS/MS based untargeted analysis is compound identification due to the limitation of MS/MS records of authentic standard. MS-FINDER aims to provide solutions for 1) formula predictions, 2) fragment annotations, and 3) structure elucidations by means of survey scan MS and MS/MS spectra of unknowns. MS- FINDER has been developed as the collaborative work between Prof. Masanori Arita team (RIKEN, Reifycs Inc.) and Prof. Oliver Fiehn team (UC Davis) supported by the JST/NSF SICORP “Metabolomics for the low carbon society” project. Hiroshi Tsugawa RIKEN Center for Sustainable Resource Science hiroshi.tsugawa@riken.jp MS-FINDER screenshot 1

Table of contents Software environments .......................................................................................................................... 4 Required programs ................................................................................................................................ 5 Acceptable ASCII formats ...................................................................................................................... 6 MSP format ........................................................................................................................................ 6 MAT format ........................................................................................................................................ 7 Adduct ion format: [M+Na]+, [M+2H]2+, [M-2H2O+H]+, [2M+FA-H]-, etc. ..................................... 9 Import queries ..................................................................................................................................... 10 A. From a folder which includes MSP or MAT format files ............................................................. 10 B. From the graphical user interface of the MS-FINDER program ................................................ 11 C. From the MS-DIAL program ....................................................................................................... 12 Analysis parameter setting ................................................................................................................. 13 Formula finder tab ........................................................................................................................... 13 Structure finder tab ......................................................................................................................... 15 Compound annotation (Single analysis) .............................................................................................. 17 Compound annotation (batch analysis) ............................................................................................... 19 Peak assignment (single) ..................................................................................................................... 20 Peak assignment (batch job) ................................................................................................................ 21 Mouse function ..................................................................................................................................... 22 Export .................................................................................................................................................. 23 Help ...................................................................................................................................................... 24 3

Software environments  Windows OS (.NET Framework 4.0 or later): Windows 7 or later  RAM: 8.0 GB or more 4

Required programs  MS-FINDER Download link: http://prime.psc.riken.jp/Metabolomics_Software/MS-FINDER/index.html  MS-FINDER can be used as the local software program in Windows PC. The program can import ASCII format files including MSP (MS/MS) or improved MSP (both MS and MS/MS, the file extension should be MAT.). In addition, the users can directly make the query in the MS- FINDER graphical user interface. Moreover, this program can be called from the MS-DIAL program which is downloadable at http://prime.psc.riken.jp/Metabolomics_Software/MS- DIAL/index.html. 5

Acceptable ASCII formats This program accepts two file extensions, i.e. MSP or MAT formatted by the following explanations. The point is that unknown queries should be separately stored in the ASCII file: the MSP or MAP file ‘CANNOT’ store multi compound records in the single file. MSP format The format of MSP basically follows the NIST MS search manual. Link: http://www.nist.gov/srd/upload/NIST1a11Ver2-0Man.pdf Required fields  NAME:  PRECURSORMZ:  PRECURSORTYPE:  IONMODE: (Positive or Negative)  SPECTRUMTYPE: (Centroid or Profile)  Num Peaks:  m/z intensity pair (tab, comma, space can be used as the delimiter.)  Mass spectrum is supposed to be imported as MS/MS.  If you want to perform the MS/MS peak annotation with the known structure, prepare two fields including FORMULA and SMILES. Please note that the formula and SMILES of the neutralized structure should be prepared. MSP example 6

MAT format The MAT format was defined as the improved version of MSP in the MS-FIDNER program to store both MS1 and MS/MS spectra in the same file. The survey scan MS data should be required to calculate ‘isotopic ion score’ for formula predictions. Required fields  NAME:  PRECURSORMZ:  PRECURSORTYPE:  IONMODE:  MSTYPE:  Num Peaks:  m/z intensity pair (tab, comma, space can be used as the delimiter.)  Three fields including MSTYPE, Num Peaks, and m/z intensity pair should be SERIALLY stored.  If you type ‘MSTYPE: MS1’, the spectrum written from next field should be recognized as the survey scan MS (MS1). If you type ‘MSTYPE: MS2’, next spectrum should be recognized as the MS/MS spectrum.  Both field (MSTYPE: MS1 and MSTYPE: MS2) is not necessary for this program, i.e. the users can import the ASCII file as only MS1 spectrum or as only MS/MS spectrum record.  Actually, the users may prepare the MAT or MSP files without any spectrum record. In such case, the formula prediction will be performed by means of mass accuracy and database criteria.  If you want to perform the MS/MS peak annotation with the known structure, prepare two fields including FORMULA and SMILES. The formula and SMILES of the neutralized structure should be made. 7

MAT example 8

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