I feel like there is a problem in your conversion. Better, validate the search parameters (which you are using at present) with some *known (may be in you lab old data file) *correct file (raw or mzml). See, to confirm if the search parameters you are using are working. If the problem still persists then you are correct .. go for asking about correct parameters for Xtandem, Spectrast and Comet ?
On Mon, Dec 14, 2020 at 9:35 PM rita maria de Almeida < [email protected]> wrote: > 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 [email protected]. > To view this discussion on the web visit > https://groups.google.com/d/msgid/spctools-discuss/54c7b11a-7cb2-447e-9ee3-f8d43d1dd842n%40googlegroups.com > <https://groups.google.com/d/msgid/spctools-discuss/54c7b11a-7cb2-447e-9ee3-f8d43d1dd842n%40googlegroups.com?utm_medium=email&utm_source=footer> > . > -- ------------------------------------------------------------------- -- 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 view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/CALZrgHSHKPxKKL%2BOg6VyDNs9TgZ3QU%3DuYPVHtmMoM%3D15CXKv6g%40mail.gmail.com.
