Unable to read mgf files

[bsakc]

log id:mmacgkfv5e00qtjsp7o96rt4pq_1719841584.log
error type:Error
message:duplicate column(s): matchscore
id: undefined

I have created the mgf files on both proteome discoverer and MSconvert however, i always get this error message and cannot see the spectra matching to the crosslinks. the csv files were produced using xisearch. Please let me know if there is an issue with my workflow

[colin-combe]

Hi,
the error message suggests there are two columns named "matchscore" in the CSV file you uploaded. It is case insensitive with regards column headers.

Please check the CSV files to see if it has two columns named 'matchscore'. If so, try deleting one of them and uploading again. Please let me know if this works or if there are still problems.

Best wishes,
Colin

[bsakc]

Hi Colin,
thank you for your quick response. I checked the csv file and there is only one column for matchscore. Is there anything else it could be?

Thanks
Adam

[colin-combe]

Hmmm.
Could you share the CSV file with me, please?
If you don't want to post your data in public here, you can email it to me at [email protected].

[colin-combe]

it could be taking spaces out of column names also, so "matchscore" and "Match Score" would count as duplicate column names

[bsakc]

Hi Colin

i tried to send you an email yesterday with the csv file but the email could not send for some reason. i have attached it here.
bsa dss_Xi1.7.6.7.csv

[bsakc]

i have seen your email about the file containing two different matchscores. which one would be best to delete?

[colin-combe]

yes... it has "MatchScore" and "match score" and the xiview parser thinks these are the same, which it maybe shouldn't do.
But the easiest thing in short term is just to delete one.
@lutzfischer might have some guidance on which is better to delete?
Or you could make an arbitrary choice just to see if it works.

[bsakc]

thank you so much for the help I'll try those now

[lutzfischer]

The right one to delete would be MatchScore.

[grandrea]

I think those columns are part of the xiSEARCH csv output, not of the xiFDR CSM file that is the one that should be uploaded to xiView. Indeed the file you have uploaded here is not the CSM file, but it's the unfiltered csv file coming out of xiSEARCH as far as I can tell. See reply Rappsilber-Laboratory/XiSearch#107

[colin-combe]

i think @bsakc has things working now.

You should upload the mzIdentML file produced by xiFDR.

Rappsilber-Laboratory/XiSearch#107 (comment)