Hi Jimmy, Is this fix included in the 5.1 release candidate that is available at the sourceforge Sashimi page? TPP_Setup_5.1.0-rc1.exe
Best, Alejandro On Wednesday, September 6, 2017 at 10:37:10 PM UTC+2, Jimmy Eng wrote: > > 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] <javascript:>> > 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] <javascript:>. >> To post to this group, send email to [email protected] >> <javascript:>. >> 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.
