Hi Alastair, If your search results are either all heavy or all light (not variable mod searched) then you should also use option -S.
1). You cannot specify anything but single amino acids in this string. Your quantitation will be based on peptides without PTMs in this dataset. 2). -r8 is a MUCH too wide window to recover the MS1 signal in RTspace. The lower this number the more selective the tool is at isolating your target signal. With -r8 you will not be quantifying the correct signal, unless you have a very bare sample. If you are able to share this data I can try running it to help you optimize your settings. Thanks, -David On Wed, Aug 5, 2020 at 11:02 AM 'Alastair Skeffington' via spctools-discuss <[email protected]> wrote: > 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 [email protected]. > To view this discussion on the web visit > https://groups.google.com/d/msgid/spctools-discuss/4853fda5-cc2f-48e2-a9e2-2ae93225b288o%40googlegroups.com > <https://groups.google.com/d/msgid/spctools-discuss/4853fda5-cc2f-48e2-a9e2-2ae93225b288o%40googlegroups.com?utm_medium=email&utm_source=footer> > . > -- 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 [email protected]. To view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/CAGJJY%3D_GKrN4Vk9LyQ%2BjkWAts5KwgXyL5gYSXFdGmO9f7fdJdw%40mail.gmail.com.
