There’s no trivial solution, I think. But here are some non-trivial possibilities:
1) Search the whole dataset with variable heavy label 2) Create a spectral library with the heavy labeled peptides and merge that library with a normal human library and search with SpectraST 3) Replace all the heavy labeled amino acids in your peptides with some letters such as B and J and then set Comet or whatever search engine to have the correct masses for B and J. 4) Eventually the optimal solution will be to use the PEFF format which can support such modifications right in the PEFF file. Comet and the TPP will support this sometime this year I hope but not super soon. 5) X!Tandem has a mechanism to specify a file containing proteins with certain mass modifications. I can’t seem to find the documentation on how to do it at the moment, but X!Tandem can do it. Regards, Eric *From:* spctools-discuss@googlegroups.com [mailto: spctools-discuss@googlegroups.com] *On Behalf Of *Sim Kae Hwan *Sent:* Thursday, March 02, 2017 10:07 PM *To:* spctools-discuss *Subject:* [spctools-discuss] Database search of heavy isotope labeled peptides Hi, I have spiked in 10 in-house heavy isotope labeled standard peptides into a non-labeled complex human peptide mixtures (trypsin-digested whole cell lysate). Can anyone advise me how to perform the database search? and also the creation of fasta database for this specific task? Many thanks! Best regards, KH -- 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 spctools-discuss+unsubscr...@googlegroups.com. To post to this group, send email to spctools-discuss@googlegroups.com. 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 spctools-discuss+unsubscr...@googlegroups.com. To post to this group, send email to spctools-discuss@googlegroups.com. Visit this group at https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
