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Philosopher: there are peptides shown to be not unique but don't have any mapped proteins #267
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Hi Masaki, I think some runs don't have any data. Such as
My guess is that these runs triggered this error
Could you please remove the runs with 0 PSM and try again? Also, there are a lot of peptides shown to be not unique but don't have any mapped proteins. Not sure if it is related. Could you please help to check if those peptides are indeed not unique but don't have any mapped proteins? Thanks, Fengchao |
HI Masaki, Regarding the randomness, I don't think the ID numbers have any randomness. The same run should have the same result. Can you double check it based on the run name? Regarding the peptide assignments, you may send some psm.tsv to us for check if you want. Best, Fengchao |
Sure. I will take a look at your files. I will also try to reproduce the error that happens when there is 0 PSMs to make IonQuant not crash in this case. Best, Fengchao |
Hi Masaki, I verified that those warning are true. Those are peptides shown to be not unique but don't have any mapped proteins: Felipe @prvst, could you take a look when you have time? Thanks, Fengchao |
Hi Fengchao, Thanks you for the verification. |
Yes, you are right. If a peptide is shown to be not unique, there should be mapped proteins. So, this is a bug and we are trying to fix it. BUT, if a peptide is shown to be unique, there MIGHT BE mapped proteins because of the definition of uniqueness in ProteinProphet. Best, Fengchao |
Hello MSFragger team,
I'm trying to run LFQ searches with MBR, but receive the error attached.
Sometimes it occurs, and somtimes it doesn't.
Each file seems to have good quantification results, but MSstats file is not produced.
What could be the cause of the error?
Thanks,
Masaki
log_2020-12-02_08-34-06.txt
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