fragment sequence alignment problem

[ZhaoTY2077]

Dear Feng Chao: here is my log file first of all: log_20240909.txt

I used modified workflow DIA_SpecLib_Quant to do proteins search and quantification with DIANN on a Linux server. the modification was only adding the path of database file(the protein sequence fasta file). After I got the quantification results by DIANN, I tried to map the precursors in result file report.pr_matrix.tsv back to the initial fasta file (that i provided to fragpipe for protein search) to see the positions of precursors.

The problem is: some of the precursors would have miss matches of the amino acid residues when doing the mapping, and most of the miss matches are 1 , only few are 2. I'm wondering if this results from the transfer of runing results between different processes? like diann have different judgement logic compare with msfragger?

I am curious about this phenomenon because I also did protein search and quantification using diann only, with same data provided. And I also tried to map the precursors back to the sequences. The results was no miss matches. (I set Missed cleavages to 1 in DIANN, not sure if this matters).

Do you have any idea why this happens to fragpipe?

Best, Troy. looking forward to your reply. ps: thanks for all your effort on developing fragpipe!

[fcyu]

When you matched the sequences, did you treat I and L the same? MSFragger doesn't distinguish I and L because they have the identical mass.

Best,

Fengchao