Thank you. I will try that. Em ter., 15 de dez. de 2020 às 01:52, sudarshan kumar < kumarsuders...@gmail.com> escreveu:
> 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 < > ritamcdealme...@gmail.com> 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 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 >> <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 a topic in the > Google Groups "spctools-discuss" group. > To unsubscribe from this topic, visit > https://groups.google.com/d/topic/spctools-discuss/gm7S-gxVo8A/unsubscribe > . > To unsubscribe from this group and all its topics, 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/CALZrgHSHKPxKKL%2BOg6VyDNs9TgZ3QU%3DuYPVHtmMoM%3D15CXKv6g%40mail.gmail.com > <https://groups.google.com/d/msgid/spctools-discuss/CALZrgHSHKPxKKL%2BOg6VyDNs9TgZ3QU%3DuYPVHtmMoM%3D15CXKv6g%40mail.gmail.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 spctools-discuss+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/CAK-hJYCqvawKDvn0wTYbixamjdLmP%2BC4-kz_k0Mpx-7BzDdNpQ%40mail.gmail.com.
