Some of the PSMs do have the corresponding scores in mzId

[ypriverol]

Describe the bug

Hi: We have been working a lot recently with MSGF+, reanalysing PRIDE data using the quantms workflow. We have detected an error in mzId export of MSGF+ (report in quantms here: bigbio/quantms#447). Looks like sometimes MSGF+ do not export the PSMs scores.

To Reproduce

Here the forlder with the mzML, the command, the FASTA file and the resulted mzID: https://ftp.pride.ebi.ac.uk/pub/databases/pride/resources/proteomes/quantms-benchmark/94508cae253c72810c2dc0200e2c3e/

• msgf command: https://ftp.pride.ebi.ac.uk/pub/databases/pride/resources/proteomes/quantms-benchmark/94508cae253c72810c2dc0200e2c3e/msgf_command.sh
• FASTA: https://ftp.pride.ebi.ac.uk/pub/databases/pride/resources/proteomes/quantms-benchmark/94508cae253c72810c2dc0200e2c3e/Homo-sapiens-uniprot-reviewed-contam-entrap-decoy-20241105.fasta
• mzML: https://ftp.pride.ebi.ac.uk/pub/databases/pride/resources/proteomes/quantms-benchmark/94508cae253c72810c2dc0200e2c3e/f07531_Prot_02_R2_F08.mzML
• mods.txt: https://ftp.pride.ebi.ac.uk/pub/databases/pride/resources/proteomes/quantms-benchmark/94508cae253c72810c2dc0200e2c3e/mods.txt