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Nesvilab
Plant proteins not appearing in output files
Describe the bug I have used MSFragger to analyse proteomics data from Arabidopsis before, but when I tried with the latest version of MSFragger (in the FragPipe wrapper), it did not return any Arabidopsis protein IDs. I only got IDs for trypsin and some proteins from humans. I don't remember changing any settings from when it has worked previously.
If you're submitting a bug report, please attach log file
Log file is attached.
It might because Philosopher cannot recognize the protein header in the fasta file.
Felipe @prvst , can you take a look when you have time?
Thanks,
Fengchao
Can you share the database with me? I'll include rules for parsing TAIR sequences. While it's not ready, I suggest you try again using sequences from NCBI.
I can't seem to share the FASTA file. I guess I could email it to you, right?
Link to fasta file. [?txt icon] athal.fasta.txthttps://uniwa-my.sharepoint.com/:t:/g/personal/00102016_uwa_edu_au/EePdff4rRyxNsl6fbZO80UIB8g2vcKQWb-xAbuVJT_KSHA?email=reply%2BANAVB3ZHDN57H7GGTSK4IEOAGPXWTEVBNHHEKMQQIQ%40reply.github.com&e=PWIeu7
From: Felipe da Veiga Leprevost @.> Sent: Tuesday, 8 March 2022 10:18 AM To: Nesvilab/FragPipe @.> Cc: Nathan Tivendale @.>; Author @.> Subject: Re: [Nesvilab/FragPipe] Plant proteins not appearing in output files (Issue #616)
Can you share the database with me? I'll include rules for parsing TAIR sequences. While it's not ready, I suggest you try again using sequences from NCBI.
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I have shared the FASTA file with you via email. Hopefully that worked.
Got it. I'll work on the format and include a new rule for the next version.
@prvst Have you added the format to the Philosopher 4.6.0?
Best,
Fengchao