Re: [ms-align-plus-pipeline] -K Option in TopPIC Not Reflecting in Output Files

[Liu, Xiaowen (Kevin)]

Hi, Ayesha,

1. How the -K option is expected to function?
• Should decoy matches explicitly appear in the output file?

With the default settings, TopPIC filters out identifications with an E-value cutoff of 0.01. If you would like to report decoy identifications, you need to use a large E-value cutoff.  For example,

toppic -d -v 10000 -V 10000 -K proteins.fasta spectra_ms2.msalign.

2. Is there a specific format or naming convention for decoy sequences in the FASTA file that TopPIC expects?

The decoy sequences have a protein name starting with DECOY_

3. Is this a known issue in the current version?

Please use the latest version is 1.7.8, in which several bugs have been fixed.

 

Please let me know if you have any other questions.

 

Best,

 

Xiaowen (Kevin)

 

From: top-dow...@googlegroups.com <top-dow...@googlegroups.com> on behalf of Ayesha Feroz <ayeshafe...@gmail.com>
Date: Friday, January 31, 2025 at 1:42 AM
To: TopPIC <top-dow...@googlegroups.com>
Subject: [ms-align-plus-pipeline] -K Option in TopPIC Not Reflecting in Output Files

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Hi, I am currently using TopPIC for proteoform identification and employing the -K option, which is expected to retain decoy identifications in the output files. However, despite including -K in my command, the decoy hits do not appear in the final proteoform.tsv or prsm.tsv output files. The command i used is toppic -d -K proteins.fasta spectra_ms2.msalign.

Could you please confirm:

1. How the -K option is expected to function?

• Should decoy matches explicitly appear in the output file?

2. Is there a specific format or naming convention for decoy sequences in the FASTA file that TopPIC expects?
3. Is this a known issue in the current version?

• I am using TopPIC v1.7.6.

 

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