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Rappsilber-Laboratory / XiSearch

XiSearch
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what are correct columns for scan number in csv files generated by xiFDR? #29

Closed ljavier2401 closed 5 years ago

ljavier2401 commented 5 years ago

Dear Prof Rappsilber and colleagues,

I am trying to follow the instructions you described in the manuscript you published in Nature protocols for performing quantitative crosslinking mass spectrometry. I have already used with success XiSearch and xiFDR. Now I am trying to filter the csv files for the identified regular and cross-linked peptides in order to generate the corresponding .ssl file to be uploaded by Skyline. The format of .ssl file very simple, a tab separated values with only four columns filename, scan, charge and peptide sequence. However, when I opened csv files, saved by xiFDR, for linear peptides and cross-linked peptides I noticed that there is two different scan numbers for each identification one is named as "scan" and the other as "scanID". What ids the correct one that I have to include in the *.ssl files? I want to be sure before to proceed further.

best regards, javier

lutzfischer commented 5 years ago

Scan - is the scan-number as reported by the masspec (actually as parsed out from the TITLE field in the mgf-file/apl-file). The scanid is the index of that scan in the file. E.g. the first scan in an mgf file will have 1 as scanid but most likely a much larger scan_number (scan)

lutzfischer commented 5 years ago

sorry just noticed I explained what is the difference but not what to use. What you want for skyline is the scan-column - as that references back to the scan in the raw file while scanid reference the position in the peaklist file.