hey guys,
I m analyzing Itraq proteome data without any idea. firstly, I sort out some uncharacterized protein and then chose the unique peptides more than 2 as a standard. Until now, I have accession, description, unique peptides, PSMs and some ratio values, however, really have no idea about how to analysis further.
Any suggestion is welcomed.
Thanks Andreas for your detailed information.
According to what you suggested, I removed those protein which are not related with my work. Further, If possible, can you share some information about ratios variability? For example, 116/115 variability %, what does this mean? and 116/115 count?
If I want to calculate P vaule, how should I do? I read some of your papers about those proteome analysis. If possible, please share with me more about it.
Cheers
Yang
For my part, you should not choose 2 as a unique peptide selection standard since some MS's data processing ability is very well. You could see the guideliness at MCP (Molecular & Cellular Proteomics) website. Further, uncharacterized protein should not be ignored, their BP, MF, and CC might be matched in subsequent bioinformatics analysis, such as Blast2Go. If necessary, you could choose 1.2 as a fold change value to filter DPEs.
Warm regards,
Jiayi
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