Build library from MSfragger output pepxml

Build library from MSfragger output pepxml af1234  2021-06-19

I have a set of 16 synthetic peptides (heavy Cterm R/K) which I ran individually and as pool in DDA on a Qexactive and searched using MSfragger. I am now trying to import the results into Skyline to build targeted assays but it seems there are some issues.

I tried the usual import DDA search to build a library but once I load the pepxml files there are not a correspondent MGF file and an error. I cannot generate a library within MSfragger because there are not enough peptides across all samples for RT alignment.

Are there some preferred settings/tricks for import MSfragger output?


Nick Shulman responded:  2021-06-19
This is the page which says which files you need for each type of peptide search results:

That page says that for msfragger you are supposed to put your pep.xml in the same folder as your .mzML, .mgf, or even raw files.

What do you mean "there are not a correspondent MGF file"? Do you have some .mzML files or raw files? Those would be expected to work as well.

-- Nick