Questions about using HBV PDC000198 dataset

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Dear PepQuery2 Developers,

I have a question about the peptides using the PDC000198 dataset. The PDC000198 is digested by trypsin. So, the end of the peptides should be K or R. But When I search the peptide such as IEEREKLVIS, we can get the result. May I know the reasons?

Thank you for your time and support.

Best regards,

[wenbostar]

The C terminal peptides from proteins may not have K or R in the end. When your input target is a peptide, we don't remove it from the search in PepQuery. We do trypsin digestion when compare the spectra matched to your input target peptide against the reference peptides from the reference proteins. For your specific case, I don't see any confident match returned:

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1. Sorry, I put an inappropriate example. Based on the paper "Integrated Proteogenomic Characterization of HBV-Related Hepatocellular Carcinoma", The proteins of the PDC000198 set are digested by trypsin. So, the detected peptides should end up with K or R. But When I search some peptides such as APRGVRMAV, we can get the result. It is confident.
2. I am setting up an experiment using isobaric labels (e.g., TMT or iTRAQ) and have a question regarding the isotope correction factors. The MaxQuant software defaults these factors to 0 for all channels. Could you please advise on how to obtain the appropriate correction factors ?

[wenbostar]

Sorry, I put an inappropriate example. Based on the paper "Integrated Proteogenomic Characterization of HBV-Related Hepatocellular Carcinoma", The proteins of the PDC000198 set are digested by trypsin. So, the detected peptides should end up with K or R. But When I search some peptides such as APRGVRMAV, we can get the result. It is confident.

As I already mentioned, a peptide from the C terminal of a protein could be ended with an amino acid which is not K/R. Where is this APRGVRMAV derived from?

I am setting up an experiment using isobaric labels (e.g., TMT or iTRAQ) and have a question regarding the isotope correction factors. The MaxQuant software defaults these factors to 0 for all channels. Could you please advise on how to obtain the appropriate correction factors ?

This seems to be a question for MaxQuant developer.

[2390735351-byte]

Sorry, I put an inappropriate example. Based on the paper "Integrated Proteogenomic Characterization of HBV-Related Hepatocellular Carcinoma", The proteins of the PDC000198 set are digested by trypsin. So, the detected peptides should end up with K or R. But When I search some peptides such as APRGVRMAV, we can get the result. It is confident.

As I already mentioned, a peptide from the C terminal of a protein could be ended with an amino acid which is not K/R. Where is this APRGVRMAV derived from?

I am setting up an experiment using isobaric labels (e.g., TMT or iTRAQ) and have a question regarding the isotope correction factors. The MaxQuant software defaults these factors to 0 for all channels. Could you please advise on how to obtain the appropriate correction factors ?

This seems to be a question for MaxQuant developer.

The peptides can be found in the uniprot database:
O95987 · O95987_HUMAN
MLMAQEALAFLMAQGAMLAAQERRVPRAAEVPGAQGQQGPRGREEAPRGVRMAVPLLRRMEGAPAGPGGRTAACFSCTSRCLSRRPWKRSWSAGSCPGMPHLSPDQGRF