Hello, I'm trying to run a 14N/15N labelling experiment through ASAPRatio. I've been running the first steps like this - here for the results of a database search with heavy masses:
InteractParser sample_interact.pep.xml sample.pep.xml PeptideProphetParser sample_interact.pep.xml RefreshParser sample_interact.pep.xml ./EhuxAllproteins_MCC_decoy.fasta ASAPRatioPeptideParser sample_interact.pep.xml -lACDEFGHIKLMNPQRSTVWY -r8 -mA72.0779R160.1857N116.1026D116.0874C104.1429E130.1140Q130.1292G58.0513H140.1393I114.1576L114.1576K130.1723M132.1961F148.1739P99.1152S89.0773T102.1038W188.0793Y164.0633V101.1311 At this point I get a warning: WARNING: Found more than one variable mod on 'M'. Please make sure to specify a heavy mass for this residue So I have two questions: 1) How do I specify the heavy mass for oxidised methionine? Mox ? And is phosphorylated serine coded Sp ? 2) I've used -r8 instead of the default 0.5. My reasoning is that a medium sized heavy peptide could easily differ from the 14N counterpart by 16 Da. Assuming charge +2, then using a m/z range of 8. Does this sound remotely sensible? Many thanks! Alastair -- 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 view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/4853fda5-cc2f-48e2-a9e2-2ae93225b288o%40googlegroups.com.
