Hi Sami, there are two kinds of SpectraST libraries, raw libraries and consensus libraries. Raw libraries may have many replicates and that’s fine. Consensus libraries will not have replicates. Replicates are converted into a consensus by SpectraST when suitable flags are set. Note that the same peptide with two different charge states are NOT replicates. Those are different, because both the precursor and the product ion spectrum are different.
Regarding different protein mappings, I believe that SpectraST has an option to remap the peptides in a library against a new FASTA file. I forget the option but you should be able to find it in the docs, I can’t view them at the moment. Let me know if you can’t find it and I’ll look. Regards, Eric *From:* [email protected] <[email protected]> *On Behalf Of *Sami Pietilä *Sent:* Thursday, May 3, 2018 6:00 AM *To:* spctools-discuss <[email protected]> *Subject:* [spctools-discuss] Duplicate peptides in consensus spectral library with different protein identifications Hi all! I am using spectrast from TPP 5.1 to generate a consensus spectral library. I noticed that the resulting library can contain the same peptide (identical sequence) multiple times. The charge stage might vary between the entries as well as the protein annotation (also originating sample can be different). Somehow it looks like a single peptide sequence can have different protein annotation in a library depending on what is the originating sample. Is this by design? I am wondering how to deal with this situation when analyzing the resulting data. Thanks -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout. -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
