Mass Analyst

Analysis of

MS(MS) data

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)

• Load mzXML data (ms-ms data)

First step is to turn the machine-vendor dependent data format into a common dataformat: 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

Load pepXML and/or mascot data

Data from several search engines (mascot/sequest etc) can beconverted to pepXML: http://sashimi.sourceforge.net/software_tpp.html

We will import pepXML (if an search had been performed) together withmzXML 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 valueof precursor ion.

! Schema’s | documentation is aviable !

Note: search engines use FASTA sequence databases to search againstWe will need these FASTA databases to retreive complete sequences of the found proteins.

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

&Display ms experiments graphicallyProvide an interactive visualization

The visualization is VERY important. It should be simple but still provide a lot of information

How and What do display?

m/z

tim

e (s

)

m/z

tim

e (s

)

this needs to be zoomable !

more detail

m/z

tim

e (s

)

CLICKABLE (if info on this point is aviable)

ms/ms

ELVISLIVESKpI: 4.5678mw: 562

protein: joda1etc…

m/z

tim

e (s

)ELVISLIVESK

pI: 4.5678mw: 562

protein: joda1etc…

LOADING MORE THAN ONE EXPERIMENT/SAMPLEs1

s2

RATIO 2.1

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

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 Dalton2 Dalton

A program with similar processes:

mzMine

http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1187873