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Mass Analyst

Mass Analyst. Analysis of MS(MS) data. Short function overview: L oad mzXML data (ms-ms data) L oad pepXML and/or mascot data (found proteins/peptides after search with the raw data C ombine both data sources D isplay ms experiments graphically P rovide an interactive visualization

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Mass Analyst

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  1. Mass Analyst Analysis of MS(MS) data

  2. Short function overview: • Load mzXML data (ms-ms data) • Load pepXML and/or mascot data (found proteins/peptides after search with the raw data • Combine both data sources • Display ms experiments graphically • Provide an interactive visualization • Quantification of data (depending on experiment) • Export results (e.g. excel table)

  3. Load mzXML data (ms-ms data) • First step is to turn the machine-vendor • dependent data format into a common data • format:  mzXML • (software avaible @ • http://sashimi.sourceforge.net/software_glossolalia.html • We will use the mzXML standard as input for our RAW data • (e.g. ms-spectra). • Parsers | Schemas | Software are aviable for using mzXML

  4. Load pepXML and/or mascot data Data from several search engines (mascot/sequest etc) can be converted to pepXML: http://sashimi.sourceforge.net/software_tpp.html We will import pepXML (if an search had been performed) together with mzXML data from the same experiment. pepXML contains: found peptides/proteins for each ms/ms spectrum this is linked to the retention time (in mzXML) and mz value of precursor ion. ! Schema’s | documentation is aviable ! Note: search engines use FASTA sequence databases to search against We will need these FASTA databases to retreive complete sequences of the found proteins.

  5. Combine both data sources • Both mzXML and pepXML are combined internally • Are we going to keep all data in XML format ? • - when loaded into the program: binary would be much faster • - exported data should be in excel (tab telimited) • - xml export -> new results in extention of pepXML

  6. & Display ms experiments graphically Provide an interactive visualization The visualization is VERY important. It should be simple but still provide a lot of information How and What do display?

  7. time (s) m/z

  8. more detail time (s) m/z this needs to be zoomable !

  9. time (s) ELVISLIVESK pI: 4.5678 mw: 562 protein: joda1 etc… m/z ms/ms CLICKABLE (if info on this point is aviable)

  10. LOADING MORE THAN ONE EXPERIMENT/SAMPLE s1 s2 time (s) ELVISLIVESK pI: 4.5678 mw: 562 protein: joda1 etc… RATIO 2.1 m/z

  11. Options in visualization • zoom • Selection on criteria • Highlight all peptides of one protein • Highlight all peptides with certain modification • etc. • Show masses, pI’s etc • Select spots/peaks to visualize more info

  12. Quantification of ms data • Quantification within one experiment (quality control) • Quantification between two experiments • Compare peak- heights/areas of extracted ion chromato. • Compare peaks from ms/ms fragmentation • Use user specified label to identify which peaks to compare 2 Dalton 4 Dalton

  13. A program with similar processes: mzMine http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1187873

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