I am planning to carry out MS for a protein sample isolated after a pull down experiment with bacterial cell lysate. I expect to get a complex of proteins against the bait protein, which can be identified during the mass spec run.
I have seen some mass spec results previously where data is presented in formats of excel formats with the name and uniproKB IDs of the identified proteins and their respective scores.
Given the possibility of observing many proteins in the spectra, what are the possible ways to format this data so that it can be compared to existing databases of protein-protein interactions(like the DIP,INTact,KEGG)
MASCOT helps you to analyse mass spec data. As you have said, generally data is presented in the form of excel sheet with the m/z ratios. Follow http://www.matrixscience.com/cgi/search_form.pl?FORMVER=2&SEARCH=SQ
In the query bar, paste your mass spec data, select appropriate databases(Generally SwissProt). Modify other parameters if required or else let it remain default.
After getting spectra with low RMS value, you can note the respective protein name and check it in either STRING or MINT.
If you have further confusions, you can ask me.
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