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compomics / compomics-utilities

Open source Java library for computational proteomics
http://compomics.github.io/projects/compomics-utilities.html
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Tag matching error at end of protein sequence, utilities-4.11.19 #26

Closed Thys3Potgieter closed 4 years ago

Thys3Potgieter commented 6 years ago

Hi Team, I have found what seems to be an error in the output of PeptideMapper: 787.369,IVAS,113.087,LNAEMGRIVASL,A0A0S3S6D4,283

However the protein sequence ends with: LNAEMGRLV, so there are three amino acids added in the identified peptide.

My IdentificationParmetersCli settings where: prec tol 0.02 in Da, and frag tolerance 0.02 in Daltons. I realize I am not using the latest version, and will let you know if I see it in the latest version when I have a chance to rerun my data.

Tag: 787.369,IVAS,113.087

Protein:

tr|A0A0S3S6D4|A0A0S3S6D4_PHAAN

Kind regards, Thys

dominik-kopczynski commented 6 years ago

Hi Thys,

thank you very much for reporting the errors :-) Can it be, that the protein sequence is not available in your previous post? I can only see the fasta header "tr|A0A0S3S6D4|A0A0S3S6D4_PHAAN". Did you use any PTMs?

Cheers, Dominik

Thys3Potgieter commented 6 years ago

tr|A0A0S3S6D4|A0A0S3S6D4_PHAAN Uncharacterized protein (Fragment) OS=Vigna angularis var. angularis GN=Vigan.05G186800 PE=4 SV=1 MKVWTLDAALQRCQWPRHFREILSQTILTGLISDPYAASRLINFSTRSALVPFDYSLRIF NHLHNPNPFTWNTIMRAHFELQNNPHQAITLYKLFLAKHAKPDNYTYPIPLQCCAARVSD FEGRELHAHVLRFGFRQDVYVRNTLINLYAICGRMSSARQVFEESPVWDLVSWNTVLAGY VQAGNVKEAERVYRGMPERNTIASNSMIVLFGRKGCVEKARRIFDEVRWRDMDMVSWSAM VSCYEQNEMCEEALVLFVEMKASGVTVDEIVVVSVVSACSRILNAEMGRLV

Thys3Potgieter commented 6 years ago

A0A0S3S6D4.fasta.gz

Thys3Potgieter commented 6 years ago

identification.par (1).zip

Thanks Dominik, the parameters are the same as my previous message. Sorry for the missing info!

dominik-kopczynski commented 6 years ago

Thank you Thys, I'll try to reproduce and fix the error ASAP :-) Cheers