Produced csv files not compatible with xisearch

[bsakc]

The csv files formed after a search on xisearch or xiFDR seem to have extra columns that causes error messages when loading with mgf files into xiview. The messages are usually unidentified columns, such as 'matchscore' or 'pepseq1'. i have been in contact with one of the creators of xiview and he belives the issue is with the csv files. I assum this is not an issue with the mgf files themselves as xisearch can run them, however, just incase i have produced mgf files from both proteome discoverer and MSconvert. I am using the basic configuration and the built in FDR on xisearch if that information is of use.

Thanks Adam

[grandrea]

Hey- could you tell me which file you are uploading into xiview? In xiView you should upload the file labelled as mysearch_CSM.csv, i.e. the FDR-filtered crosslinked spectra matches. You can also upload the mzIdentML instead. So the xiview upload should be mgf files, a .fasta, and the CSM file coming out of xiFDR or the mzIdentmL.

[colin-combe]

hi Andrea,

In xiView you should upload the file labelled as mysearch_CSM.csv, i.e. the FDR-filtered crosslinked spectra matches. You can also upload the mzIdentML instead.

You should upload the mzIdentML file produced by xiFDR.

i think it says that on the xiVIEW upload page but i will make the message more prominent.

ultimately @bsakc is correct, the CSV files are not compatible. You will see -1 for the experimental m/z and calculated mass, and then wrong values for things calculated from those. https://github.com/Rappsilber-Laboratory/xiFDR/issues/33