Dear all, I hope this is the right list for my question. I played a little bit with the recent TPP and the Mix 7 (Orbitrap) from http://regis-web.systemsbiology.net/PublicDatasets/ I have some questions:
1. Is the protein composition identical with the publication ? The TPP identified for example insulin with prob = 0.99. Insulin is not mentioned in the paper (http://regis-web.systemsbiology.net/PublicDatasets/database/ProteinMixDatasetPaper.pdf). 2. I have some problems to understand the programs behind the web framework. I performed a database search with Mascot 2.1 and swissprot. After the search I converted the 10 dat files from mascot to pepXML. With the given dataset I started the same analysis in two different ways. A) I started 10 PeptideProphet runs (the Mix7 has 10 fractions). After that the ProteinProphet runs with 10 files in the command line. B) I started one PeptideProphet run with 10 files and one ProteinProphet run with the result file. The comparison of the two result files shows differences (1549 protein groups vs. 1484 protein groups or 33 protein groups vs. 34 protein groups with prob >= 0.9) Is there any explanation for the differences and what is the right way for one experiment ? Thanks for help. Cheers Marco -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
