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snijderlab / stitch

Template-based assembly of proteomics short reads for de novo antibody sequencing and repertoire profiling
MIT License
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Support MaxQuant database search input data #238

Open douweschulte opened 1 year ago

douweschulte commented 1 year ago

Allowing users to read in MaxQuant database searches would allow some nice analyses we normally do on de novo data to be done on database data with a bit more certainty of the data correctness. msms.txt WP

Ln9052 commented 9 months ago

Hi,

Recently, I have encountered an issue when using Stitch to read the msmsScan.txt file generated by Maxnovo. The error reported is "Line has too low amount of fields (70)." Additionally, I attempted to use Stitch to read the msms.txt file provided in your last comments , but encountered the same error. In my understanding, this error indicates that there is a low number of fields during the data parsing process starting from the second line. Have you also observed this issue? Furthermore, do you have any suggestions or methods for resolving this issue?

Thank you!

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douweschulte commented 9 months ago

Currently there is no support for any msms.txt file generated by Maxquant either in de novo or database matching function. The msmsScans.txt file generated after de novo analysis is the only file supported, so in that case if the file does not work please send it to me so I can see what the problem is.

Ln9052 commented 9 months ago

Thank you for your response. Could you please take a look at file msmsScans.txt and help me to identify the cause of the issue mentioned above? Thank you once more for your assistance.

douweschulte commented 9 months ago

MaxNovo seems to have changed their format a little bit. I fixed up the code in stitch that reads in these files to allow for this newer format. See the most recent nightly build to have this fix applied.

Ln9052 commented 9 months ago

Thank you very much, following your instructions, Stitch successfully read the Maxnovo file.