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.
