Stpeter

[sudarshan kumar]

Anyone can please explain-

1. Does Stpeter SIn value represent a ratio between control and treated files?

2. I understand that all the files /MS runs are integrated to make one .prot file after the protein prophet analysis.

3. So in StPeter how do we know the SIn score for a particular protein is for which sample (control or treatment)

4. Does StPeter has option of grouping proteins sample wise or run file wise?

5. Or do we need to run protein prophet separately for control and treatment and then do StPeter run separately for these two files of control and treatment and then calculate the relative ratio of SIn between control and treatment in excel.

Best 

[mhoo...@systemsbiology.org]

1. No - see your other thread (https://groups.google.com/g/spctools-discuss/c/yDBVf5nHxmM) for a lengthy explanation. 

2/3. You don't. Quantities for any protein in a prot.xml file are obtain from the sums of all PSMs that were combined to make that prot.xml file. To split protein quantities by sample in StPeter, it is best to conduct individual analyses for each sample such that each sample will have its own prot.xml file.

4/5. Yes, run protein prophet separately for control and treatment, then run StPeter on those two files, then compute the ratio of SIn between control and treatment, just as you describe in #5.

Cheers,

Mike