Hi there, I am new at the analyses on proteomics. I am analysing a set of experiments I retrieved from Peptide atlas. The organism is Homo sapiens, and it has been made available in 2013, using Exactive orbitrap from Thermo Scientific. They comprise 3 replicates and were fractioned 3 times. So each condition has 8 or 9 samples (some of them did not pass the quality control, I guess).
It is possible to retrieve both mzXml and raw data. I have retrieved both. I searched with Xtandem, Spectrast and Comet using Petunia interface. All three performed 0 spetctra searches. I have produced mzml files from the raw data using Petunia. Again, all three (Xtandem, Spectrast, and Comet) resulted 0 searches. I have used a APD.Hs.all.fasta, retrieved form PeptideAtlas, as the sequence database. I guess maybe it could be the parameter values I have used (I used default and those values suggested in the TPP tutorial using Saccharomyces cerevisae (demo2009)). So, my question is Where can I get information on how to select the correct parameters for Xtandem, Spectrast and Comet ? -- 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 view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/54c7b11a-7cb2-447e-9ee3-f8d43d1dd842n%40googlegroups.com.
