24601_file1.txt

1. use msconvert to convert files from RAW to mzXML.
2. use x!tandem and comet to search the files.
3. peptideProphet and iProphet were used to combine search results from different search engines.
4. ProteinProphet was used to generate a post-probability for each protein/proteoform group, which was further converted into a table by prot2xls.
5. a simple R script was made to generate the final submitted table.