Yes this release is from code revision 7625 which includes Jimmy's patch. -David
On Fri, Sep 22, 2017 at 8:07 AM, Jimmy Eng <[email protected]> wrote: > Alejandro, > > I don't know what made it into the 5.1.0-rc1 binary so I can't answer that > question. Someone at ISB will hopefully be able to chime in. > > On Fri, Sep 22, 2017 at 2:43 AM, Alejandro <[email protected]> wrote: > >> 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]> 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. >> > > -- > 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. 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