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. m/z time (s)

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

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

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

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 4 Dalton 2 Dalton

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