Oded, I just checked in a fix for the issue. It will hopefully be available in the next TPP 5.1.0 release whenever that happens.
Jimmy On Thu, Aug 31, 2017 at 7:00 AM, Oded <[email protected]> wrote: > Hi there, > I am trying to do run a quantitative analysis of dimethylated samples > labelled on N-term and lysine (using either trypsin or ArgC) using TPP ver5 > on Windows. > I ran X!Tandem or Comet searches using fixed light di-Met modification of > Lys and N-term (+28.03) and the Heavy-Light delta (6.031) as variable > modifications as explained here, and I used successfully before. > Quantification with XPRESS run without any error but the ratio calculation > seems to be correct only for peptides that contain a lysine (regardless if > they were heavy or light). The ratio calculated for peptides that do not > contain lysines is correct only for the light labelled ones but for the > heavy ones the program seems to consider them as light peptides and > searches for peaks that are +6 heavier in order to calculate the ratio. > For example if we got the peptide AAAHTSPR that was identified in the > light dimethylation on the N-term, MH= 838.4530) the program will look for > the heavy couple at the right place (MH=844.4848) but if the same peptide > was identified in its heavy form (MH 838.4530) it seems like the program is > looking for the heavy partner at 844.4848. > Another minor (?) comment is that running such searches with X!tandem > seems to mark the heavy N-term dimethylation in a different way than it > used to before (and currently appear in Comet pepxml) add looks like this: > n7.04A99.07TAGDTHLGGEDFDNR (instead of n35.07 > <http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?CMD=Web&LAYOUT=TwoWindows&AUTO_FORMAT=Semiauto&ALIGNMENTS=50&ALIGNMENT_VIEW=Pairwise&CDD_SEARCH=on&CLIENT=web&COMPOSITION_BASED_STATISTICS=on&DATABASE=nr&DESCRIPTIONS=100&ENTREZ_QUERY=%28none%29&EXPECT=1000&FILTER=L&FORMAT_OBJECT=Alignment&FORMAT_TYPE=HTML&I_THRESH=0.005&MATRIX_NAME=BLOSUM62&NCBI_GI=on&PAGE=Proteins&PROGRAM=blastp&SERVICE=plain&SET_DEFAULTS.x=41&SET_DEFAULTS.y=5&SHOW_OVERVIEW=on&END_OF_HTTPGET=Yes&SHOW_LINKOUT=yes&QUERY=ATAGDTHLGGEDFDNR> > ATAGDTHLGGEDFDNR. > <http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?CMD=Web&LAYOUT=TwoWindows&AUTO_FORMAT=Semiauto&ALIGNMENTS=50&ALIGNMENT_VIEW=Pairwise&CDD_SEARCH=on&CLIENT=web&COMPOSITION_BASED_STATISTICS=on&DATABASE=nr&DESCRIPTIONS=100&ENTREZ_QUERY=%28none%29&EXPECT=1000&FILTER=L&FORMAT_OBJECT=Alignment&FORMAT_TYPE=HTML&I_THRESH=0.005&MATRIX_NAME=BLOSUM62&NCBI_GI=on&PAGE=Proteins&PROGRAM=blastp&SERVICE=plain&SET_DEFAULTS.x=41&SET_DEFAULTS.y=5&SHOW_OVERVIEW=on&END_OF_HTTPGET=Yes&SHOW_LINKOUT=yes&QUERY=ATAGDTHLGGEDFDNR> > I hope you can advise. > Thanks > Oded > > -- > 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 post to this group, send email to [email protected]. > Visit this group at https://groups.google.com/group/spctools-discuss. > For more options, visit https://groups.google.com/d/optout. > -- 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 post to this group, send email to [email protected]. Visit this group at https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
