Oded, I didn't spend any time looking at the X!Tandem output at all. If there are still problems with X!Tandem and XPRESS, let me know and I'll see if I can fix them.
Jimmy On Tue, Sep 26, 2017 at 3:43 AM, Oded <oded.kleif...@gmail.com> wrote: > Thank you all. From a quick check it seems that things are working well > now with Comet. > With X!tandem as I mentioned in my orignal post the heavy N-term is > annotated just as the mass difference relative to the light plus the amino > acid mass and therefore is different for each amino acid but I think XPRESS > ratios are correct. > Thanks again, > Oded > > On Friday, September 22, 2017 at 7:22:39 PM UTC+3, David Shteynberg wrote: >> >> 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 <jke...@gmail.com> 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 <agome...@gmail.com> 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 <oded.k...@gmail.com> 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 spctools-discu...@googlegroups.com. >>>>>> To post to this group, send email to spctools...@googlegroups.com. >>>>>> 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 spctools-discu...@googlegroups.com. >>>> To post to this group, send email to spctools...@googlegroups.com. >>>> 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 spctools-discu...@googlegroups.com. >>> To post to this group, send email to spctools...@googlegroups.com. >>> 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 spctools-discuss+unsubscr...@googlegroups.com. > To post to this group, send email to spctools-discuss@googlegroups.com. > 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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