Hi Eric, Thank you! The parameter seems to be -cD. Now the protein annotations are the same for identical peptide sequences.
BR, Sami perjantai 4. toukokuuta 2018 4.07.38 UTC+3 Eric Deutsch kirjoitti: > > 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] <javascript:> < > [email protected] <javascript:>> *On Behalf Of *Sami Pietilä > *Sent:* Thursday, May 3, 2018 6:00 AM > *To:* spctools-discuss <[email protected] <javascript:>> > *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] <javascript:>. > To post to this group, send email to [email protected] > <javascript:>. > 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.
