The total mass of the modified amino-acid / terminus is specified to ASAPRatio. The unmodified n-terminus of any peptide is 1.007825 (or the mass of H), since your termini are modified the mass of the modification will be added to 1.0078.
Also, please update to the latest version of the TPP (4.4.1) . Thanks, -David On Tue, Jan 11, 2011 at 10:23 AM, gkayihan <gochemo...@gmail.com> wrote: > Hi all, > I have been trying to quantify our dimethyl labeled samples for the > last week using TPP. I got it to work when I ran heavy and light label > SEQUEST searches separate and in ASAP ratio I chose the option of > "static modification quantification" and chose K and n-terminus as the > "labeled residues" . I chose the option of " use fixed scan range for > light and heavy". Then set m/z range to "0.05". > At this point I put monoisotopic mass of K with the dimethyl heavy > label (164.01706) to the "specified residue mass". I tried adding n- > terminus as 36.0757 but it says I have three different masses for n- > terminus (29.0388, 36.0757 and 37.0838) so I used only K with > dimethylation (heavy). It runs without a hitch but during the run it > says n terminus is labeled with 29.0388 and 37.0838. Why does is give > a protonated N-terminus for heavy and light label ? K seems to have > the right numbers for heavy and light labels. > > I am using windows 7, TPP v 4.3 jetstream rev 1 build 200909091257 > (MinGW) and we are using an LTQ Orbitrap. > The command line is below, I would really appreciate all the help. > cheers > Gogce Crynen > > # Commands for session 9UNL73SYC on Tue Jan 11 13:12:34 2011 > # BEGIN COMMAND BLOCK > ###### BEGIN Command Execution ###### > [Tue Jan 11 13:12:34 2011] EXECUTING: run_in c:/Inetpub/wwwroot/ISB/ > data/111610_crudeLYSATE_SIDL_1to1/HandL; c:\Inetpub\tpp-bin\xinteract > -N111610_crudeLYSATE_SIDL_1to1_Rep1_L_H2.pep.xml -p0.05 -l7 -OAp -A- > lKn-F-r0.05-S-mK164.1706 c:/Inetpub/wwwroot/ISB/data/ > 111610_crudeLYSATE_SIDL_1to1/HandL/ > 111610_crudeLYSATE_SIDL_1to1_Rep1_H.pep.xml c:/Inetpub/wwwroot/ISB/ > data/111610_crudeLYSATE_SIDL_1to1/HandL/ > 111610_crudeLYSATE_SIDL_1to1_Rep1_L.pep.xml > OUTPUT: > > c:\Inetpub\tpp-bin\xinteract (TPP v4.3 JETSTREAM rev 1, Build > 200909091257 (MinGW)) > > running: "C:/Inetpub/tpp-bin/InteractParser > "111610_crudeLYSATE_SIDL_1to1_Rep1_L_H2.pep.xml" "c:/Inetpub/wwwroot/ > ISB/data/111610_crudeLYSATE_SIDL_1to1/HandL/ > 111610_crudeLYSATE_SIDL_1to1_Rep1_H.pep.xml" "c:/Inetpub/wwwroot/ISB/ > data/111610_crudeLYSATE_SIDL_1to1/HandL/ > 111610_crudeLYSATE_SIDL_1to1_Rep1_L.pep.xml" -L"7"" > file 1: c:/Inetpub/wwwroot/ISB/data/111610_crudeLYSATE_SIDL_1to1/ > HandL/111610_crudeLYSATE_SIDL_1to1_Rep1_H.pep.xml > file 2: c:/Inetpub/wwwroot/ISB/data/111610_crudeLYSATE_SIDL_1to1/ > HandL/111610_crudeLYSATE_SIDL_1to1_Rep1_L.pep.xml > processed altogether 34720 results > > > results written to file c:/Inetpub/wwwroot/ISB/data/ > 111610_crudeLYSATE_SIDL_1to1/HandL/ > 111610_crudeLYSATE_SIDL_1to1_Rep1_L_H2.pep.xml > > direct your browser to > http://localhost/ISB/data/111610_crudeLYSATE_SIDL_1to1/HandL/111610_crudeLYSATE_SIDL_1to1_Rep1_L_H2.pep.shtml > > > > command completed in 6 sec > > running: "C:/Inetpub/tpp-bin/PeptideProphetParser > "111610_crudeLYSATE_SIDL_1to1_Rep1_L_H2.pep.xml" MINPROB=0.05 ACCMASS" > using Accurate Mass Bins > (SEQUEST) > adding Accurate Mass mixture distr > init with SEQUEST trypsin > MS Instrument info: Manufacturer: Thermo Scientific, Model: LTQ > Orbitrap, Ionization: ESI, Analyzer: FTMS, Detector: unknown > > PeptideProphet (TPP v4.3 JETSTREAM rev 1, Build 200909091257 > (MinGW)) akel...@isb > read in 71 1+, 9098 2+, 7422 3+, 228 4+, 22 5+, 0 6+, and 0 7+ > spectra. > Initialising statistical models ... > Iterations: .........10.........20.........30... > WARNING: Mixture model quality test failed for charge (1+). > model complete after 34 iterations > command completed in 21 sec > > running: "C:/Inetpub/tpp-bin/ProphetModels.pl -i > 111610_crudeLYSATE_SIDL_1to1_Rep1_L_H2.pep.xml" > Analyzing 111610_crudeLYSATE_SIDL_1to1_Rep1_L_H2.pep.xml ... > Reading Accurate Mass Model model +1 ... > Reading Accurate Mass Model model +2 ... > Reading Accurate Mass Model model +3 ... > Reading Accurate Mass Model model +4 ... > Reading Accurate Mass Model model +5 ... > Reading Accurate Mass Model model +6 ... > Reading Accurate Mass Model model +7 ... > Parsing search results "c:/Inetpub/wwwroot/ISB/data/ > 111610_crudeLYSATE_SIDL_1to1/HandL/111610_crudeLYSATE_SIDL_1to1_Rep1_H > (SEQUEST)"... > => Total of 999 hits. > Parsing search results "c:/Inetpub/wwwroot/ISB/data/ > 111610_crudeLYSATE_SIDL_1to1/HandL/111610_crudeLYSATE_SIDL_1to1_Rep1_L > (SEQUEST)"... > => Total of 836 hits. > command completed in 1 sec > > running: "C:/Inetpub/tpp-bin/ASAPRatioPeptideParser > "111610_crudeLYSATE_SIDL_1to1_Rep1_L_H2.pep.xml" -lKn -F -r0.05 -S - > mK164.1706" > K 156.126 164.171 > n 29.0388 37.0838 > static heavy label for file c:/Inetpub/wwwroot/ISB/data/ > 111610_crudeLYSATE_SIDL_1to1/HandL/ > 111610_crudeLYSATE_SIDL_1to1_Rep1_H.mzXML > static light label for file c:/Inetpub/wwwroot/ISB/data/ > 111610_crudeLYSATE_SIDL_1to1/HandL/ > 111610_crudeLYSATE_SIDL_1to1_Rep1_L.mzXML > command completed in 35 sec > > running: "C:/Inetpub/tpp-bin/DatabaseParser > "111610_crudeLYSATE_SIDL_1to1_Rep1_L_H2.pep.xml"" > command completed in 1 sec > > running: "C:/Inetpub/tpp-bin/RefreshParser > "111610_crudeLYSATE_SIDL_1to1_Rep1_L_H2.pep.xml" "C:\Xcalibur\database > \ipi.MOUSE.v3.72.fasta"" > - Searching the tree... > - Linking duplicate entries... - Printing results... > > - Building Commentz-Walter keyword tree...command completed in 4 > sec > > running: "c:/Inetpub/wwwroot/../tpp-bin/PepXMLViewer.cgi -I c:/Inetpub/ > wwwroot/ISB/data/111610_crudeLYSATE_SIDL_1to1/HandL/ > 111610_crudeLYSATE_SIDL_1to1_Rep1_L_H2.pep.xml" > command completed in 1 sec > > running: "C:/Inetpub/tpp-bin/ProteinProphet > "111610_crudeLYSATE_SIDL_1to1_Rep1_L_H2.pep.xml" > "111610_crudeLYSATE_SIDL_1to1_Rep1_L_H2.prot.xml" XML" > ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the > original Perl by A. Keller (TPP v4.3 JETSTREAM rev 1, Build > 200909091257 (MinGW)) > (xml input) (report Protein Length) (using degen pep info) > . . . reading in c:/Inetpub/wwwroot/ISB/data/ > 111610_crudeLYSATE_SIDL_1to1/HandL/ > 111610_crudeLYSATE_SIDL_1to1_Rep1_L_H2.pep.xml. . . > . . . read in 14 1+, 1011 2+, 752 3+, 21 4+, 2 5+, 0 6+, 0 7+ spectra > with min prob 0.05 > INFO: mu=3.55413e-005, db_size=51125798 > > protein probabilities written to file c:/Inetpub/wwwroot/ISB/data/ > 111610_crudeLYSATE_SIDL_1to1/HandL/ > 111610_crudeLYSATE_SIDL_1to1_Rep1_L_H2.prot.xml > direct your browser to > http://localhost/ISB/data/111610_crudeLYSATE_SIDL_1to1/HandL/111610_crudeLYSATE_SIDL_1to1_Rep1_L_H2.prot.shtml > > command completed in 3 sec > > running: "C:/Inetpub/tpp-bin/ProtProphModels.pl -i > 111610_crudeLYSATE_SIDL_1to1_Rep1_L_H2.prot.xml" > Analyzing 111610_crudeLYSATE_SIDL_1to1_Rep1_L_H2.prot.xml ... > command completed in 0 sec > > running: "C:/Inetpub/tpp-bin/ASAPRatioProteinRatioParser > "111610_crudeLYSATE_SIDL_1to1_Rep1_L_H2.prot.xml"" > command completed in 111 sec > > running: "C:/Inetpub/tpp-bin/ASAPRatioPvalueParser > "111610_crudeLYSATE_SIDL_1to1_Rep1_L_H2.prot.xml"" > command completed in 2 sec > C:/Inetpub/tpp-bin/InteractParser > "111610_crudeLYSATE_SIDL_1to1_Rep1_L_H2.pep.xml" "c:/Inetpub/wwwroot/ > ISB/data/111610_crudeLYSATE_SIDL_1to1/HandL/ > 111610_crudeLYSATE_SIDL_1to1_Rep1_H.pep.xml" "c:/Inetpub/wwwroot/ISB/ > data/111610_crudeLYSATE_SIDL_1to1/HandL/ > 111610_crudeLYSATE_SIDL_1to1_Rep1_L.pep.xml" -L"7" 6 sec > C:/Inetpub/tpp-bin/PeptideProphetParser > "111610_crudeLYSATE_SIDL_1to1_Rep1_L_H2.pep.xml" MINPROB=0.05 ACCMASS > 21 sec > C:/Inetpub/tpp-bin/ProphetModels.pl -i > 111610_crudeLYSATE_SIDL_1to1_Rep1_L_H2.pep.xml 1 sec > C:/Inetpub/tpp-bin/ASAPRatioPeptideParser > "111610_crudeLYSATE_SIDL_1to1_Rep1_L_H2.pep.xml" -lKn -F -r0.05 -S - > mK164.1706 35 sec > C:/Inetpub/tpp-bin/DatabaseParser > "111610_crudeLYSATE_SIDL_1to1_Rep1_L_H2.pep.xml" > C:/Inetpub/tpp-bin/RefreshParser > "111610_crudeLYSATE_SIDL_1to1_Rep1_L_H2.pep.xml" "C:\Xcalibur\database > \ipi.MOUSE.v3.72.fasta" 4 sec > c:/Inetpub/wwwroot/../tpp-bin/PepXMLViewer.cgi -I c:/Inetpub/wwwroot/ > ISB/data/111610_crudeLYSATE_SIDL_1to1/HandL/ > 111610_crudeLYSATE_SIDL_1to1_Rep1_L_H2.pep.xml 1 sec > C:/Inetpub/tpp-bin/ProteinProphet > "111610_crudeLYSATE_SIDL_1to1_Rep1_L_H2.pep.xml" > "111610_crudeLYSATE_SIDL_1to1_Rep1_L_H2.prot.xml" XML 3 sec > C:/Inetpub/tpp-bin/ProtProphModels.pl -i > 111610_crudeLYSATE_SIDL_1to1_Rep1_L_H2.prot.xml 0 sec > C:/Inetpub/tpp-bin/ASAPRatioProteinRatioParser > "111610_crudeLYSATE_SIDL_1to1_Rep1_L_H2.prot.xml" 111 sec > C:/Inetpub/tpp-bin/ASAPRatioPvalueParser > "111610_crudeLYSATE_SIDL_1to1_Rep1_L_H2.prot.xml" 2 sec > job completed in 185 sec > END OUTPUT > RETURN CODE:0 > ###### End Command Execution ###### > # All finished at Tue Jan 11 13:15:39 2011 > # END COMMAND BLOCK > > -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To post to this group, send email to spctools-disc...@googlegroups.com. > To unsubscribe from this group, send email to > spctools-discuss+unsubscr...@googlegroups.com. > 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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