Problems in search

[rita maria de Almeida]

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 ?

[sudarshan kumar]

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 ?  

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[rita maria de Almeida]

Thank you. I will try that.

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