Default output format. Conversi on software. Conversion output formats

Transcription

1 Machine Vendor Manufact urer software Default output format Conversi on software Conversion output formats UPLC Waters Masslynx.RAW directory Wolf *.mzxml, *.cdf.raw QTOF Waters Masslynx directory Wolf *.mzxml, *.cdf LC-MS Waters Masslynx.RAW directory Wolf *.mzxml, *.cdf LC-MS Waters (TOF, (micromas Masslynx Masslynx Ultima) s) V 4.0 (.raw files) MetAlign netcdf Thermo XConvert, *.dat, *.ms, *.spa, *.raw, GC-TOF Scientific XCalibur.RAW file ReAdW *.cdf, *.txt, *.mzxml Thermo XConvert, *.dat, *.ms, *.spa, *.raw, GC-MS Scientific XCalibur.RAW file ReAdW *.cdf, *.txt, t *.mzxml LTQ-FT Thermo Scientific XCalibur.RAW file XConvert *.dat, *.cdf, *.txt LTQ- Oribtrap Thermo Scientific XCalibur.RAW file XConvert *.dat, *.cdf, *.txt LTQ Thermo Scientific XCalibur.RAW file XConvert *.dat, *.cdf, *.txt TSQ Thermo Scientific XCalibur.RAW file XConvert *.dat, *.cdf, *.txt Thermo DECA Scientific XCalibur.RAW file XConvert *.dat, *.cdf, *.txt UPLC Thermo Scientific XCalibur GC-MS Masshunt Agilent/HP er.d directory Trapper(?), mzstar (now mzwiff, beta) *.mzxml GC-MS (Quadrup HP HPchemst ool) (Agilent) ation.d UPLC Agilent Chemstati on CE Agilent Chemstati on.d file Chemstati on *.cdf GC-MS Agilent Chemstati on.d file Chemstati on *.netcdf GC-MS chromato peg (TOF) Leco F (pegasus) NetCDF GC-MS (Quadrup ool, SPME) Interscien ce XCalibur.raw NetCDF Applied BioSystem Analyst QTOF s QS.wiff file.raw GC-TOF Waters Masslynx directory.d microtof Bruker Hystar directory File Translator *.cdf DataAnaly sis *.cdf, *.txt

2 MOST WANTED MZXML CONVERTERS MassSpecWavelet Mass spectrum processing by wavelet-based algorithms XCMS Framework for processing and visualization of chromatographically separated and singlespectra mass spectral data. Imports from AIA/ANDI NetCDF, mzxml, and mzdata files. Preprocesses data for high-throughput, untargeted analyte profiling. Pedrioli PGA, Eng JK, Hubley R, Vogelzang M, Deutsch EW, Raught B, Pratt B, Nilsson E, Angeletti R, Apweiler R, Cheung K, Costello CE, Hermjakob H, Huang S, Julian RK Jr, Kapp E, McComb ME, Oliver SG, Omenn G, Paton NW, Simpson R, Smith R, Taylor CF, Zhu W, Aebersold R. (2004) "A Common Open Representation of Mass Spectrometry Data and its Application in a Proteomics Research Environment." Nature Biotechnology 22(11):

3 TPP relatives msconvert: general data format conversion tool. msdiff: comparison of two data files, for validation of conversion and preprocessing mscat: exports data from a variety of formats into 4 column text format Each vendor data coversion job was done in commandline and through webinterface. Peaks where extracted from commandline generated mzxml files and TPP gui generated mzxml files. Peaks where parsed to ASCII with mscat. Msdiff was used to compare ASCII commandline data versus ASCII webinterface data.

4 Mzxml webinterface generated vs commandline generated vs netcdf vs.raw data comparisons

5 Mass++ can read and process various MS data format. However the commercially attached software with MS machines is required to read some of data formats.applied Biosystems (QSTAR)... "Analyst QS" should be installed. - Applied Biosystems (QTRAP)... "Analyst" should be installed. - ThemoFisher h (LCQ /LTQ / LTQFT / Orbitrap)... "XCalibur" " should be installed. - Waters (QTOF)... "MassLynx" should be installed. - Shimadzu (LCMS-IT-TOF)... "LCMSsolution DataExportModules" should be installed. - Shimadzu (GCMS)... "GCMSsolution" should be installed.

6 X2XML The X2XML program will read different mass spectrometry data files and create an mzxml file representation of the data (provided the proper vendor software is installed). It is an extension of the ReAdW application to support the following file formats: Xcalibur.RAW files Agilent.wiff files Micromass.DAT files (inside.raw folders) Bruker.acqu files Bruker ASCII.ascii files PNNL ion-mobility spectrometry (IMS).imf files Bruker FTICR S-folders, which are a single-file per spectrum representation of the large "s" files created by Bruker FTICR instruments. (This file format is the predominant format used to store Bruker FTICR data at PNNL)

7

8

9

10

11

12

13

14 / ReAdW ReAdW ReAdW-4.0. ReAdW-3.5.4_b ReAdW ReAdW ReAdW ReAdW ( => FilterrLine metadata slot) ReAdW_2006Nov01 (mzxml xsd v 2.0) ReAdW-src_2006Nov01 sashimi/

15

16

17

18

19

20

21

22

23

24

25

26

27

28

29

30

31

32

33

34

35

36

37

38

39

40

41

42

43

44

45

46

47

48

49

50

51

52

53

54

55

56

57