Hi, I am planning to do LFQ using ProteinQuantifier from OpenMS, which can take ProteinProphet results as the identification input. However, for the data (human proteome data from PRIDE) that I am processing, there is a huge gap between output from ProteinProphet and MAYU, and I am thinking about using MAYU (if reasonable) to filter the protein IDs. My question is, is there any way to convert MAYU's result into protXML?
PS: For 24 runs, ProteinProphet gives 5245 entries (1966 single hits) with IPROPHET option MAYU produces mFDR IP/PPs protFDR TP_protID TP_protIDs TP_protIDns protFDRns 0 0.999996 0 6867 2918 3949 0 0.001 0.789611 0.006219 11332 3851 7481 0.001598 0.002 0.387495 0.013356 11639 3869 7771 0.00378 0.003 0.172753 0.020108 11917 3956 7963 0.005627 0.004 0.115397 0.026528 12003 3953 8052 0.007476 0.005 0.073709 0.033135 12090 3946 8146 0.008813 0.006 0.050291 0.039517 12185 3964 8223 0.010479 0.007 0.037582 0.044578 12268 3971 8299 0.011241 0.008 0.028534 0.051116 12322 3953 8371 0.01285 0.009 0.022003 0.056202 12415 3981 8436 0.014644 0.01 0.017422 0.062456 12480 3989 8494 0.015794 Thanks, -Han . -- 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 post to this group, send email to spctools-discuss@googlegroups.com. Visit this group at http://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
