Hi Brian, Thanks for the input. Yes, it depends on how the search was performed. I tested with out specifying the mass for a SILAC sample and it seemed to work. If you have different mass labels for heavy and light and the light is not specified as a static mod then you have to do what you showed in your commandline. Ultimately, it is always a good idea to verify for yourself that the masses it uses are the correct ones.
Cheers, -David On Tue, Jun 12, 2012 at 1:08 PM, Brian Hampton <[email protected]> wrote: > David, > > I am doing very similar work as Alex where light and heavy labels are on K > and the N-terminus of the peptides. In the Tandem parameters file, the > modifications are specified according the the API description from Tandem > for residue modification mass and allows to search with two different > labels on the same residue. > > residue, modification mass Lightmod@K, Lightmod@[ > residue, potential modification mass Heavymod-Lightmod@K, > Heavymod-Lightmod@[ > In my case Lightmod=42.024 and Heavymod=48.028 > > In ASAPRatio, if I do not specify a modification mass (as you seem to > suggest below) for the amino acids it matches up the pairs incorrectly. > Rather than finding labeled pairs of peptides differing by 6u, it finds > light labeled and *unlabeled* pairs differing by 42u, which doesn't exist. > > So I specify n and K in the "Change modified residues to" since the > N-terminus and K are the only labeled residues and then I specify all four > labeled residue masses with their respective monoisotopic masses of 42 & 48 > for n and 170.0124 and 170.0125 for K. Then it seems to work. Maybe it > works differently with input from another search engine, I don't know. > > I am guessing the following warning is informational only and doesn't > indicate something is wrong: > > running: "/usr/local/apps/tpp/bin/ASAPRatioPeptideParser > 'BH_2-interact.pep.xml' -lnK -b -r0.5 -mn42.024n48.028K170.0124K176.0125" > WARNING: Found more than one variable mod on 'K'. Please make sure to specify > a heavy mass for this residue. > > Thanks in advance for any help here. > > Brian > > > On Mon, Jun 11, 2012 at 4:02 PM, David Shteynberg < > [email protected]> wrote: > >> Hi Alex, >> >> If your tandem search used monoisotopic masses for the variable mods then >> you don't really have to specify the masses and it will use the mass in the >> file. ASAPRatio allows you to redefine the mass (so you can use average >> masses for matching fragments and monoisotopic for quantitation), if the >> pep.xml file alread has the monoisotopic masses listed then you can just >> specify the labeled amino acids and those will be applied to find the >> heavy/light pairs. Let me know if you require further clarification. >> >> Cheers, >> -David >> >> On Mon, Jun 11, 2012 at 12:47 PM, Alex <[email protected]> wrote: >> >>> Quick question, probably directed to David, >>> >>> I've used ASAPratio by following through a couple of posts, trying to >>> figure out how to complete the options on Petunia. It still remains a >>> little unclear why or what should be completed in the fields: >>> Change labeled residues to >>> Specified residue mass 1: >>> I work with dimethylated labels (formaldehyde reagent targeting free >>> amino groups and its 'heavy' deuterated D2CO form) and understand I should >>> add K and n as the "change labeled residues" and add the mass of the heavy >>> residues to the "specified residue mass" (n=33.06425 and K=160.15137 for >>> the deuterium modified labels). This has so far worked out to me. >>> >>> My question is why should they be added to both fields? Is this >>> redundant or is there any case where one could add a modification to one >>> field and not the other? I have added all the modifications (light and >>> heavy labels) to the X!Tandem parameters files, including other modifs as >>> alkylated cystesines and oxidized M and all the peptides have been >>> correctly identified. Judging by the previous posts, this has caused >>> confusion to other ASAPratio users in the past. >>> >>> And a suggestion: it would be very convenient to have a 'zoom' and >>> 'unzoom' option when viewing the results on the ASAPratio viewer. >>> Sometimes, ASAPratio offers a very narrow window of the integrated peak, >>> and I find viewing the axis in a larger window is good to assess how >>> specific the XIC looks for a particular precursor along the complete >>> chromtographic run. >>> >>> Thanks TTP people, hope to hearing back from you!!! >>> >>> Alex >>> >>> -- >>> You received this message because you are subscribed to the Google >>> Groups "spctools-discuss" group. >>> To view this discussion on the web visit >>> https://groups.google.com/d/msg/spctools-discuss/-/mJrJOy17rKQJ. >>> To post to this group, send email to [email protected]. >>> To unsubscribe from this group, send email to >>> [email protected]. >>> For more options, visit this group at >>> http://groups.google.com/group/spctools-discuss?hl=en. >>> >> >> -- >> You received this message because you are subscribed to the Google Groups >> "spctools-discuss" group. >> To post to this group, send email to [email protected]. >> To unsubscribe from this group, send email to >> [email protected]. >> For more options, visit this group at >> http://groups.google.com/group/spctools-discuss?hl=en. >> > > -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To post to this group, send email to [email protected]. > To unsubscribe from this group, send email to > [email protected]. > For more options, visit this group at > http://groups.google.com/group/spctools-discuss?hl=en. > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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