Importing data from FragPipe

[witszymanski]

Hi all, After speaking with Nesvilab, they encouraged me to write to you guys.

So, I tried to import combined.pep.xml with .mgf files created by both FragPipe itself and by http://fields.scripps.edu/rawconv/ and it doesn't work (set of 9 .raw files) The message is always:

Then I tried to upload a single file from psm.tsv with the .mgf from FragPipe and this works:

However, when I combine few psm.tsv together and add multiple .mgf files, it fails again:

Any idea, how to upload more than 1 raw file at once?

All the best! Greets Witek

[KaiLiCn]

Hi Witek,

Sorry for the inconvenience. Could you please share your files with me? You know, sometimes after converting the raw files, the software might make some changes in the spectrum file. So, I am not very clear what's the exact problem. But I can take a look this week.

Kai

[witszymanski]

Hi Kai! Thanks for the reply! With single file ADPR-5-1_calibrated.mgf and single psm1.tsv it works. It doesn't work If I want to upload more than 1 file into PDV or if I use combined.pep.xml file.

All the data you can find here: https://owncloud.gwdg.de/index.php/s/HQUpL80r0GyoxoK password: pdv

Greets Witek

[KaiLiCn]

Got it. I will take a look and hopefully fix it this week.

Kai

[KaiLiCn]

Hi Witek,

Could you please convert the raw files to .mzML? It should work when you input one combined .tsv result from FragPipe and multiple .mzML files. Since there is no direct relationship between results files and raw files, especially when users convert the format, it's complicated to map a single spectrum back to each raw file. However, I am working on this part.

Please try the solution I mentioned and let me know if you meet any new problems.

Kai