Re: [spctools-discuss] Changes in number of peptides identifications in TPP 6.0 RC
Hi David, This time I used *xinteract -NinteractDecoyCount.pep.xml -p0.05 -l7 -PPM -OANEdp -dDECOY0 Seq69478_QE2.pep.xml. * With TPP 5.2 the count of DECOY1 ids at 1% error rate is 84 and the total count of DECOY ids is 151 (out of 7102 PSMs). With TPP 6.0 the count of DECOY1 ids at 1% error rate is 7 and the total count of DECOY ids is 9 (out of 5308 PSMs). You can find the new interact files here:https://www.dropbox.com/t/s7ZqgkP1f0Yzl0Xn. Many thanks, Oded On Wednesday, 14 April 2021 at 08:34:42 UTC+3 David Shteynberg wrote: > Hi Oded, > > I think the old 5.2.0 might be under estimating the error rate as compared > to the new release candidate. You cannot see the decoys here because of > the settings you used. However your database has two independent sets of > decoys available DECOY0 and DECOY1. Can you use one of the set for > PeptideProphet and use the other set to get a decoy count at a given > PeptideProphet probability cutoff. I suspect the 5.2.0 TPP will show more > unknown decoys than the new release candidate. Can you test if this is > the case here? I can run a more in depth analysis when I am back from > vacation next week. > > Cheers, > David > > On Tue, Apr 13, 2021, 2:07 PM Oded wrote: > >> Dear David, >> This is PeptideProphet issue (we don't use iProphet for this analysis). >> With the search parameters that I sent you followed by running the >> PeptideProphet command of *xinteract -Ninteract.pep.xml -p0.05 -l7 -PPM >> -OANEp -dDECOY Seq69478_QE2.pep.xml,* >> and lastly using a cutoff of 1% error rate we obtain with TPP 5.2 2836 >> correct assignments and with TPP 6.0 only 2228 correct assignments. The >> probability for 1% error rate is 0.84 in TPP 5.2 and 0.9090 in TPP 6.0). >> In the following link, you will find the interact files (new and old): >> https://www.dropbox.com/t/mwtpCLeEJRLCwbi1 >> <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.dropbox.com%2Fl%2FAACfc2b_KukHZAS1VuNo4sPM3gEXyXtDlPE=04%7C01%7Coklab%40technion.ac.il%7C342d2db781c2443416b108d8febfbc70%7Cf1502c4cee2e411c9715c855f6753b84%7C1%7C0%7C637539447557029368%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000=LBdAB3QsH9rUxvNKMwKjOKYDbQXFxma9dREKgS5siWQ%3D=0> >> Thanks, >> Oded >> >> >> >> On Tuesday, 13 April 2021 at 03:38:33 UTC+3 David Shteynberg wrote: >> >>> Dear Oded, >>> >>> Thanks for this. I ran a quick test and I actually observed a few more >>> PSMs for PeptideProphet 6.0.0-rc14 for the same PeptideProphet probability >>> cutoff for this dataset. Is the issue you see with PeptideProphet or >>> iProphet results? Which spectra were getting excluded in the your testing >>> of 5.2.0 vs 6.0.0, can you give me some specific examples? Are you certain >>> you are using identical analysis parameters for PeptideProphet and what are >>> those parameters? >>> >>> Cheers, >>> >>> David >>> >>> On Mon, Apr 12, 2021, 2:15 PM Oded wrote: >>> >>>> And also the search results with the new vs the old version (although I >>>> think they are more or less the same): >>>> https://www.dropbox.com/t/8VyBVdeuoWdk982q >>>> >>>> >>>> On Tuesday, 13 April 2021 at 00:09:05 UTC+3 Oded wrote: >>>> >>>>> Hi David, >>>>> You can find the mzML, Comet parameters and FASTA file here: >>>>> https://www.dropbox.com/t/Yld0ZBWhsuFajeLj >>>>> The link is valid for 7 days. >>>>> Many thanks, >>>>> Oded >>>>> >>>>> On Monday, 12 April 2021 at 23:46:08 UTC+3 David Shteynberg wrote: >>>>> >>>>>> I don't mind taking a crack at it over vacation. Please let me know >>>>>> where I can pull the data from. I might not have quick solution for you >>>>>> but >>>>>> I can get started looking for the problem. Which search engine did you >>>>>> use >>>>>> here? I would need mzML data search results and the fasta database to >>>>>> get >>>>>> started. >>>>>> >>>>>> Thanks! >>>>>> >>>>>> >>>>>> >>>>>> Thanks! >>>>>> >>>>>> On Mon, Apr 12, 2021, 1:38 PM Oded wrote: >>>>>> >>>>>>> Hi David, >>>>>>> Thank you for the quick reply. We are using TPP v6.0.0-rc14 >>>&
Re: [spctools-discuss] Changes in number of peptides identifications in TPP 6.0 RC
Dear David, This is PeptideProphet issue (we don't use iProphet for this analysis). With the search parameters that I sent you followed by running the PeptideProphet command of *xinteract -Ninteract.pep.xml -p0.05 -l7 -PPM -OANEp -dDECOY Seq69478_QE2.pep.xml,* and lastly using a cutoff of 1% error rate we obtain with TPP 5.2 2836 correct assignments and with TPP 6.0 only 2228 correct assignments. The probability for 1% error rate is 0.84 in TPP 5.2 and 0.9090 in TPP 6.0). In the following link, you will find the interact files (new and old): https://www.dropbox.com/t/mwtpCLeEJRLCwbi1 <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.dropbox.com%2Fl%2FAACfc2b_KukHZAS1VuNo4sPM3gEXyXtDlPE=04%7C01%7Coklab%40technion.ac.il%7C342d2db781c2443416b108d8febfbc70%7Cf1502c4cee2e411c9715c855f6753b84%7C1%7C0%7C637539447557029368%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000=LBdAB3QsH9rUxvNKMwKjOKYDbQXFxma9dREKgS5siWQ%3D=0> Thanks, Oded On Tuesday, 13 April 2021 at 03:38:33 UTC+3 David Shteynberg wrote: > Dear Oded, > > Thanks for this. I ran a quick test and I actually observed a few more > PSMs for PeptideProphet 6.0.0-rc14 for the same PeptideProphet probability > cutoff for this dataset. Is the issue you see with PeptideProphet or > iProphet results? Which spectra were getting excluded in the your testing > of 5.2.0 vs 6.0.0, can you give me some specific examples? Are you certain > you are using identical analysis parameters for PeptideProphet and what are > those parameters? > > Cheers, > > David > > On Mon, Apr 12, 2021, 2:15 PM Oded wrote: > >> And also the search results with the new vs the old version (although I >> think they are more or less the same): >> https://www.dropbox.com/t/8VyBVdeuoWdk982q >> >> >> On Tuesday, 13 April 2021 at 00:09:05 UTC+3 Oded wrote: >> >>> Hi David, >>> You can find the mzML, Comet parameters and FASTA file here: >>> https://www.dropbox.com/t/Yld0ZBWhsuFajeLj >>> The link is valid for 7 days. >>> Many thanks, >>> Oded >>> >>> On Monday, 12 April 2021 at 23:46:08 UTC+3 David Shteynberg wrote: >>> >>>> I don't mind taking a crack at it over vacation. Please let me know >>>> where I can pull the data from. I might not have quick solution for you >>>> but >>>> I can get started looking for the problem. Which search engine did you >>>> use >>>> here? I would need mzML data search results and the fasta database to >>>> get >>>> started. >>>> >>>> Thanks! >>>> >>>> >>>> >>>> Thanks! >>>> >>>> On Mon, Apr 12, 2021, 1:38 PM Oded wrote: >>>> >>>>> Hi David, >>>>> Thank you for the quick reply. We are using TPP v6.0.0-rc14 >>>>> Noctilucent, Build 202103031119-8400 (Windows_NT-x86_64). >>>>> As for the data let me know when you are back and I will transfer you >>>>> either the raw file or the search results. >>>>> Enjoy your vacation. >>>>> Thanks, >>>>> Oded >>>>> On Monday, 12 April 2021 at 22:17:53 UTC+3 David Shteynberg wrote: >>>>> >>>>>> Hi Oded, Which release candidate are you referring to? The earlier >>>>>> candidates may have a bug that is corrected in a later version. If you >>>>>> can >>>>>> share some data and specifics about the missing PSMs I can run it here >>>>>> and >>>>>> troubleshoot the problem. >>>>>> >>>>>> Thanks! >>>>>> >>>>>> David >>>>>> >>>>>> P.S. I am on vacation this week so will troubleshoot next week. >>>>>> >>>>>> On Mon, Apr 12, 2021, 11:49 AM Oded wrote: >>>>>> >>>>>>> Hi there, >>>>>>> We recently download the TPP 6.0 RC and while using it we noticed >>>>>>> that we obtain fewer peptides IDs than what we got for the same dataset >>>>>>> and >>>>>>> search output with version 5.2. >>>>>>> Many of the missing peptides seem to have decent Expect value and >>>>>>> MS/MS following a visual inspection. >>>>>>> This seems that this is due to changes in PeptideProphet and are not >>>>>>> related to the search itself that was done with Comet. >>>
Re: [spctools-discuss] Changes in number of peptides identifications in TPP 6.0 RC
And also the search results with the new vs the old version (although I think they are more or less the same): https://www.dropbox.com/t/8VyBVdeuoWdk982q On Tuesday, 13 April 2021 at 00:09:05 UTC+3 Oded wrote: > Hi David, > You can find the mzML, Comet parameters and FASTA file here: > https://www.dropbox.com/t/Yld0ZBWhsuFajeLj > The link is valid for 7 days. > Many thanks, > Oded > > On Monday, 12 April 2021 at 23:46:08 UTC+3 David Shteynberg wrote: > >> I don't mind taking a crack at it over vacation. Please let me know >> where I can pull the data from. I might not have quick solution for you but >> I can get started looking for the problem. Which search engine did you use >> here? I would need mzML data search results and the fasta database to get >> started. >> >> Thanks! >> >> >> >> Thanks! >> >> On Mon, Apr 12, 2021, 1:38 PM Oded wrote: >> >>> Hi David, >>> Thank you for the quick reply. We are using TPP v6.0.0-rc14 Noctilucent, >>> Build 202103031119-8400 (Windows_NT-x86_64). >>> As for the data let me know when you are back and I will transfer you >>> either the raw file or the search results. >>> Enjoy your vacation. >>> Thanks, >>> Oded >>> On Monday, 12 April 2021 at 22:17:53 UTC+3 David Shteynberg wrote: >>> >>>> Hi Oded, Which release candidate are you referring to? The earlier >>>> candidates may have a bug that is corrected in a later version. If you can >>>> share some data and specifics about the missing PSMs I can run it here and >>>> troubleshoot the problem. >>>> >>>> Thanks! >>>> >>>> David >>>> >>>> P.S. I am on vacation this week so will troubleshoot next week. >>>> >>>> On Mon, Apr 12, 2021, 11:49 AM Oded wrote: >>>> >>>>> Hi there, >>>>> We recently download the TPP 6.0 RC and while using it we noticed that >>>>> we obtain fewer peptides IDs than what we got for the same dataset and >>>>> search output with version 5.2. >>>>> Many of the missing peptides seem to have decent Expect value and >>>>> MS/MS following a visual inspection. >>>>> This seems that this is due to changes in PeptideProphet and are not >>>>> related to the search itself that was done with Comet. >>>>> Is there any additional parameter that should be included in the new >>>>> version in order to restore the missing peptides? >>>>> Many 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 view this discussion on the web visit >>>>> https://groups.google.com/d/msgid/spctools-discuss/b7c2e3b7-3061-4ec7-94d8-f70e43538f2an%40googlegroups.com >>>>> >>>>> <https://groups.google.com/d/msgid/spctools-discuss/b7c2e3b7-3061-4ec7-94d8-f70e43538f2an%40googlegroups.com?utm_medium=email_source=footer> >>>>> . >>>>> >>>> -- >>> 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 view this discussion on the web visit >>> https://groups.google.com/d/msgid/spctools-discuss/7f5e47e5-56df-4552-88ca-b6d4396f3d8en%40googlegroups.com >>> >>> <https://groups.google.com/d/msgid/spctools-discuss/7f5e47e5-56df-4552-88ca-b6d4396f3d8en%40googlegroups.com?utm_medium=email_source=footer> >>> . >>> >> -- 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 view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/3baf2dd3-f237-4c9d-82a2-54d563ccf5e6n%40googlegroups.com.
Re: [spctools-discuss] Changes in number of peptides identifications in TPP 6.0 RC
Hi David, You can find the mzML, Comet parameters and FASTA file here:https://www.dropbox.com/t/Yld0ZBWhsuFajeLj The link is valid for 7 days. Many thanks, Oded On Monday, 12 April 2021 at 23:46:08 UTC+3 David Shteynberg wrote: > I don't mind taking a crack at it over vacation. Please let me know > where I can pull the data from. I might not have quick solution for you but > I can get started looking for the problem. Which search engine did you use > here? I would need mzML data search results and the fasta database to get > started. > > Thanks! > > > > Thanks! > > On Mon, Apr 12, 2021, 1:38 PM Oded wrote: > >> Hi David, >> Thank you for the quick reply. We are using TPP v6.0.0-rc14 Noctilucent, >> Build 202103031119-8400 (Windows_NT-x86_64). >> As for the data let me know when you are back and I will transfer you >> either the raw file or the search results. >> Enjoy your vacation. >> Thanks, >> Oded >> On Monday, 12 April 2021 at 22:17:53 UTC+3 David Shteynberg wrote: >> >>> Hi Oded, Which release candidate are you referring to? The earlier >>> candidates may have a bug that is corrected in a later version. If you can >>> share some data and specifics about the missing PSMs I can run it here and >>> troubleshoot the problem. >>> >>> Thanks! >>> >>> David >>> >>> P.S. I am on vacation this week so will troubleshoot next week. >>> >>> On Mon, Apr 12, 2021, 11:49 AM Oded wrote: >>> >>>> Hi there, >>>> We recently download the TPP 6.0 RC and while using it we noticed that >>>> we obtain fewer peptides IDs than what we got for the same dataset and >>>> search output with version 5.2. >>>> Many of the missing peptides seem to have decent Expect value and MS/MS >>>> following a visual inspection. >>>> This seems that this is due to changes in PeptideProphet and are not >>>> related to the search itself that was done with Comet. >>>> Is there any additional parameter that should be included in the new >>>> version in order to restore the missing peptides? >>>> Many 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 view this discussion on the web visit >>>> https://groups.google.com/d/msgid/spctools-discuss/b7c2e3b7-3061-4ec7-94d8-f70e43538f2an%40googlegroups.com >>>> >>>> <https://groups.google.com/d/msgid/spctools-discuss/b7c2e3b7-3061-4ec7-94d8-f70e43538f2an%40googlegroups.com?utm_medium=email_source=footer> >>>> . >>>> >>> -- >> 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 view this discussion on the web visit >> https://groups.google.com/d/msgid/spctools-discuss/7f5e47e5-56df-4552-88ca-b6d4396f3d8en%40googlegroups.com >> >> <https://groups.google.com/d/msgid/spctools-discuss/7f5e47e5-56df-4552-88ca-b6d4396f3d8en%40googlegroups.com?utm_medium=email_source=footer> >> . >> > -- 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 view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/fe1043c4-1182-46a2-8584-63dfe13b46e3n%40googlegroups.com.
Re: [spctools-discuss] Changes in number of peptides identifications in TPP 6.0 RC
Hi David, Thank you for the quick reply. We are using TPP v6.0.0-rc14 Noctilucent, Build 202103031119-8400 (Windows_NT-x86_64). As for the data let me know when you are back and I will transfer you either the raw file or the search results. Enjoy your vacation. Thanks, Oded On Monday, 12 April 2021 at 22:17:53 UTC+3 David Shteynberg wrote: > Hi Oded, Which release candidate are you referring to? The earlier > candidates may have a bug that is corrected in a later version. If you can > share some data and specifics about the missing PSMs I can run it here and > troubleshoot the problem. > > Thanks! > > David > > P.S. I am on vacation this week so will troubleshoot next week. > > On Mon, Apr 12, 2021, 11:49 AM Oded wrote: > >> Hi there, >> We recently download the TPP 6.0 RC and while using it we noticed that we >> obtain fewer peptides IDs than what we got for the same dataset and search >> output with version 5.2. >> Many of the missing peptides seem to have decent Expect value and MS/MS >> following a visual inspection. >> This seems that this is due to changes in PeptideProphet and are not >> related to the search itself that was done with Comet. >> Is there any additional parameter that should be included in the new >> version in order to restore the missing peptides? >> Many 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 view this discussion on the web visit >> https://groups.google.com/d/msgid/spctools-discuss/b7c2e3b7-3061-4ec7-94d8-f70e43538f2an%40googlegroups.com >> >> <https://groups.google.com/d/msgid/spctools-discuss/b7c2e3b7-3061-4ec7-94d8-f70e43538f2an%40googlegroups.com?utm_medium=email_source=footer> >> . >> > -- 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 view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/7f5e47e5-56df-4552-88ca-b6d4396f3d8en%40googlegroups.com.
[spctools-discuss] Changes in number of peptides identifications in TPP 6.0 RC
Hi there, We recently download the TPP 6.0 RC and while using it we noticed that we obtain fewer peptides IDs than what we got for the same dataset and search output with version 5.2. Many of the missing peptides seem to have decent Expect value and MS/MS following a visual inspection. This seems that this is due to changes in PeptideProphet and are not related to the search itself that was done with Comet. Is there any additional parameter that should be included in the new version in order to restore the missing peptides? Many 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-discuss+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/b7c2e3b7-3061-4ec7-94d8-f70e43538f2an%40googlegroups.com.
[spctools-discuss] Dimethylation quantification with XPRESS (TPP 5.0)
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:n7.04A 99.07TAGDTHLGGEDFDNR (instead of n35.07 <http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?CMD=Web=TwoWindows_FORMAT=Semiauto=50_VIEW=Pairwise_SEARCH=on=web_BASED_STATISTICS=on=nr=100_QUERY=%28none%29=1000=L_OBJECT=Alignment_TYPE=HTML_THRESH=0.005_NAME=BLOSUM62_GI=on=Proteins=blastp=plain_DEFAULTS.x=41_DEFAULTS.y=5_OVERVIEW=on_OF_HTTPGET=Yes_LINKOUT=yes=ATAGDTHLGGEDFDNR> ATAGDTHLGGEDFDNR. <http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?CMD=Web=TwoWindows_FORMAT=Semiauto=50_VIEW=Pairwise_SEARCH=on=web_BASED_STATISTICS=on=nr=100_QUERY=%28none%29=1000=L_OBJECT=Alignment_TYPE=HTML_THRESH=0.005_NAME=BLOSUM62_GI=on=Proteins=blastp=plain_DEFAULTS.x=41_DEFAULTS.y=5_OVERVIEW=on_OF_HTTPGET=Yes_LINKOUT=yes=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-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.
[spctools-discuss] PTM prophet and DiMethylation
Hi all,
I am using TPP 4.7.1 on Win7 and currently trying to analyze data of
dimethylated phosphopeptides searched with X!tandem.
The searches were done by using 2 sets of fixed modifications for the Cys
alkylation plus light or heavy dimethylation on N-term and K with STY
phosphorylation, Met-Ox and protein N-term acetylation as set as variable
modifications.
When I try to run PTM prophet (following peptide prophet and iprophet runs)
I getting the following error:
EXECUTING: run_in c:/Inetpub/wwwroot/ISB/data/Oded/Enzo/Phospho_June2014;
c:\Inetpub\tpp-bin\PTMProphetParser
STY,79.966,C,57.021464,n,34.063117,K,34.063117,M,15.99 MZTOL=0.1
c:/Inetpub/wwwroot/ISB/data/Oded/Enzo/Phospho_June2014/interactNative1.ipro.pep.xml
interactNative
INFO: Writing file interactNative1.ptm.pep.xml ...
INFO: Reading file
c:/Inetpub/wwwroot/ISB/data/Oded/Enzo/Phospho_June2014/interactNative1.ipro.pep.xml
...
WARNING: Cannot initialize for sequence: n[71]M[147]KDEPRSTNLFMK, unknown
mods may exist in spectrum CHH20140618_M1HTiO2_100mM.03738.03738.2
WARNING: Cannot initialize for sequence: n[35]K[162]S[167]PAAAR, unknown
mods may exist in spectrum CHH20140618_M1HTiO2_100mM.03900.03900.2
WARNING: Cannot initialize for sequence: n[35]VPS[167]RHINIGR, unknown mods
may exist in spectrum CHH20140618_M1HTiO2_100mM.04358.04358.2
WARNING: Cannot initialize for sequence:
n[35]EGEEPT[181]VYSDEEEPK[162]DESAR, unknown mods may exist in spectrum
CHH20140618_M1HTiO2_100mM.04499.04499.3
WARNING: Cannot initialize for sequence: n[35]GTPGPAVR, unknown mods may
exist in spectrum CHH20140618_M1HTiO2_100mM.05584.05584.2
WARNING: Unrecognized mod on peptide: n[35]SCFESS[167]PDPELK[162]
WARNING: Unrecognized mod on peptide: n[35]SCFESS[167]PDPELK[162]
WARNING: Unrecognized mod on peptide: n[35]SCFESS[167]PDPELK[162]
WARNING: Unrecognized mod on peptide: n[35]SCFESS[167]PDPELK[162]
WARNING: Unrecognized mod on peptide: n[35]SCFESS[167]PDPELK[162]
WARNING: Unrecognized mod on peptide: n[35]SCFESS[167]PDPELK[162]
{this appear 100-200 times}
This application has requested the Runtime to terminate it in an unusual
way.
Please contact the application's support team for more information.
command c:\Inetpub\tpp-bin\PTMProphetParser
STY,79.966,C,57.021464,n,34.063117,K,34.063117,M,15.99 MZTOL=0.1
c:/Inetpub/wwwroot/ISB/data/Oded/Enzo/Phospho_June2014/interactNative1.ipro.pep.xml
interactNative1.ptm.pep.xml failed: No such process
I tried adding both heavy and light dimethylation (+28 and +34 on K and
N-term) just light and just heavy (as shown above), the the mass of the
DiMet N-term as it appear in the pepXML (+35 or +29) but the error is
still the same...
Is there a way to sort this?
Many thanks,
Oded
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[spctools-discuss] Re: Building on OS X 10.7.3
Thanks Ulrich. As always - you got it! All the best, Oded On Feb 3, 7:31 pm, Ulrich auf dem Keller uadkel...@me.com wrote: Hi Oded, the workaround is to comment out conditions for LITTLE_ENDIAN in /extern/ProteoWizard/pwiz/pwiz/utility/misc/endian.hpp: change to: // #if (defined(PWIZ_GCC) defined(__BYTE_ORDER) __BYTE_ORDER==__LITTLE_ENDIAN) || \ // (defined(__DARWIN_BYTE_ORDER) __DARWIN_BYTE_ORDER==__DARWIN_LITTLE_ENDIAN) || \ // (defined(__DARWIN_10_6_AND_LATER) defined(__LITTLE_ENDIAN__)) || \ // (defined(__MINGW32__)) || \ // (defined(__i386__)) || \ // (defined(PWIZ_MSVC)) #define PWIZ_LITTLE_ENDIAN // #endif // #if (defined(PWIZ_GCC) defined(__BYTE_ORDER) __BYTE_ORDER==__BIG_ENDIAN) // #define PWIZ_BIG_ENDIAN // #endif #if defined(PWIZ_LITTLE_ENDIAN) defined(PWIZ_BIG_ENDIAN) #error This isn't happening. #endif #if !defined(PWIZ_LITTLE_ENDIAN) !defined(PWIZ_BIG_ENDIAN) #error Unsupported platform: probably need a platform-specific define above. #endif changing DARWIN_10_6 to 10_7 didn't help. Maybe, someone figured out the correct platform definition for 10.7? Cheers Ulrich On 2012-02-03, at 6:20 AM, Oded wrote: Hi all, I trying to build version TPP 4.5.1 on OS X 10.7.3 and after make all I end up getting the following: g++ -D__LINUX__ -DDEFAULT_TPP_INSTALL_ROOT=\/usr/local/tpp/\ - D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D__INTEL__ -DINLINING - DTPPLIB -fPIC -I. -I/Users/OK/Downloads/TPP-4.5.1/ trans_proteomic_pipeline/src/. -I/Users/OK/Downloads/TPP-4.5.1/ trans_proteomic_pipeline/src/../extern/gzstream -I/Users/OK/Downloads/ TPP-4.5.1/trans_proteomic_pipeline/src/../extern -I/Users/OK/Downloads/ TPP-4.5.1/trans_proteomic_pipeline/src/../build/darwin/ libarchive-2.2.7/libarchive -I/Users/OK/Downloads/TPP-4.5.1/ trans_proteomic_pipeline/src/../build/darwin/expat-2.0.1/lib -I/Users/ OK/Downloads/TPP-4.5.1/trans_proteomic_pipeline/src/../extern/ boost_1_45_0/boost -I/Users/OK/Downloads/TPP-4.5.1/ trans_proteomic_pipeline/src/../extern/boost_1_45_0 -I/Users/OK/ Downloads/TPP-4.5.1/trans_proteomic_pipeline/src/. -I/Users/OK/ Downloads/TPP-4.5.1/trans_proteomic_pipeline/src/../build/darwin/ fann-2.0.0/src/include -I/Users/OK/Downloads/TPP-4.5.1/ trans_proteomic_pipeline/src/../build/darwin/gsl-1.14 -I /opt/local/ include/ -iprefix /Users/OK/Downloads/TPP-4.5.1/ trans_proteomic_pipeline/src/../extern/ProteoWizard/pwiz/ -iwithprefix pwiz/data/msdata -iwithprefix pwiz/data -I/Users/OK/Downloads/ TPP-4.5.1/trans_proteomic_pipeline/src/../extern/ProteoWizard/pwiz - iwithprefix pwiz -iwithprefix pwiz/utility/misc -iwithprefix pwiz/ utility/math -I/Users/OK/Downloads/TPP-4.5.1/trans_proteomic_pipeline/ src/../extern/boost_1_45_0/boost -I/Users/OK/Downloads/TPP-4.5.1/ trans_proteomic_pipeline/src/../extern/boost_1_45_0 -I/Users/OK/ Downloads/TPP-4.5.1/trans_proteomic_pipeline/src/. -iwithprefix libraries/boost_aux -I/Users/OK/Downloads/TPP-4.5.1/ trans_proteomic_pipeline/src/Parsers/ramp -iwithprefix libraries/ libsvm-3.0 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE - DPWIZ_USER_VERSION_INFO_H=\common/TPPVersion.h\ -c -O2 -o /Users/ OK/Downloads/TPP-4.5.1/trans_proteomic_pipeline/src/../build/darwin/ Serializer_mzXML.pwiz.o /Users/OK/Downloads/TPP-4.5.1/ trans_proteomic_pipeline/src/../extern/ProteoWizard/pwiz/pwiz/data/ msdata/Serializer_mzXML.cpp g++ -D__LINUX__ -DDEFAULT_TPP_INSTALL_ROOT=\/usr/local/tpp/\ - D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D__INTEL__ -DINLINING - DTPPLIB -fPIC -I. -I/Users/OK/Downloads/TPP-4.5.1/ trans_proteomic_pipeline/src/. -I/Users/OK/Downloads/TPP-4.5.1/ trans_proteomic_pipeline/src/../extern/gzstream -I/Users/OK/Downloads/ TPP-4.5.1/trans_proteomic_pipeline/src/../extern -I/Users/OK/Downloads/ TPP-4.5.1/trans_proteomic_pipeline/src/../build/darwin/ libarchive-2.2.7/libarchive -I/Users/OK/Downloads/TPP-4.5.1/ trans_proteomic_pipeline/src/../build/darwin/expat-2.0.1/lib -I/Users/ OK/Downloads/TPP-4.5.1/trans_proteomic_pipeline/src/../extern/ boost_1_45_0/boost -I/Users/OK/Downloads/TPP-4.5.1/ trans_proteomic_pipeline/src/../extern/boost_1_45_0 -I/Users/OK/ Downloads/TPP-4.5.1/trans_proteomic_pipeline/src/. -I/Users/OK/ Downloads/TPP-4.5.1/trans_proteomic_pipeline/src/../build/darwin/ fann-2.0.0/src/include -I/Users/OK/Downloads/TPP-4.5.1/ trans_proteomic_pipeline/src/../build/darwin/gsl-1.14 -I /opt/local/ include/ -iprefix /Users/OK/Downloads/TPP-4.5.1/ trans_proteomic_pipeline/src/../extern/ProteoWizard/pwiz/ -iwithprefix pwiz/data/msdata -iwithprefix pwiz/data -I/Users/OK/Downloads/ TPP-4.5.1/trans_proteomic_pipeline/src/../extern/ProteoWizard/pwiz - iwithprefix pwiz -iwithprefix pwiz/utility/misc -iwithprefix pwiz/ utility/math -I/Users/OK/Downloads/TPP-4.5.1/trans_proteomic_pipeline/ src/../extern/boost_1_45_0/boost -I/Users/OK/Downloads/TPP-4.5.1
[spctools-discuss] Building on OS X 10.7.3
Hi all, I trying to build version TPP 4.5.1 on OS X 10.7.3 and after make all I end up getting the following: g++ -D__LINUX__ -DDEFAULT_TPP_INSTALL_ROOT=\/usr/local/tpp/\ - D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D__INTEL__ -DINLINING - DTPPLIB -fPIC -I. -I/Users/OK/Downloads/TPP-4.5.1/ trans_proteomic_pipeline/src/. -I/Users/OK/Downloads/TPP-4.5.1/ trans_proteomic_pipeline/src/../extern/gzstream -I/Users/OK/Downloads/ TPP-4.5.1/trans_proteomic_pipeline/src/../extern -I/Users/OK/Downloads/ TPP-4.5.1/trans_proteomic_pipeline/src/../build/darwin/ libarchive-2.2.7/libarchive -I/Users/OK/Downloads/TPP-4.5.1/ trans_proteomic_pipeline/src/../build/darwin/expat-2.0.1/lib -I/Users/ OK/Downloads/TPP-4.5.1/trans_proteomic_pipeline/src/../extern/ boost_1_45_0/boost -I/Users/OK/Downloads/TPP-4.5.1/ trans_proteomic_pipeline/src/../extern/boost_1_45_0 -I/Users/OK/ Downloads/TPP-4.5.1/trans_proteomic_pipeline/src/. -I/Users/OK/ Downloads/TPP-4.5.1/trans_proteomic_pipeline/src/../build/darwin/ fann-2.0.0/src/include -I/Users/OK/Downloads/TPP-4.5.1/ trans_proteomic_pipeline/src/../build/darwin/gsl-1.14 -I /opt/local/ include/ -iprefix /Users/OK/Downloads/TPP-4.5.1/ trans_proteomic_pipeline/src/../extern/ProteoWizard/pwiz/ -iwithprefix pwiz/data/msdata -iwithprefix pwiz/data -I/Users/OK/Downloads/ TPP-4.5.1/trans_proteomic_pipeline/src/../extern/ProteoWizard/pwiz - iwithprefix pwiz -iwithprefix pwiz/utility/misc -iwithprefix pwiz/ utility/math -I/Users/OK/Downloads/TPP-4.5.1/trans_proteomic_pipeline/ src/../extern/boost_1_45_0/boost -I/Users/OK/Downloads/TPP-4.5.1/ trans_proteomic_pipeline/src/../extern/boost_1_45_0 -I/Users/OK/ Downloads/TPP-4.5.1/trans_proteomic_pipeline/src/. -iwithprefix libraries/boost_aux -I/Users/OK/Downloads/TPP-4.5.1/ trans_proteomic_pipeline/src/Parsers/ramp -iwithprefix libraries/ libsvm-3.0 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE - DPWIZ_USER_VERSION_INFO_H=\common/TPPVersion.h\ -c -O2 -o /Users/ OK/Downloads/TPP-4.5.1/trans_proteomic_pipeline/src/../build/darwin/ Serializer_mzXML.pwiz.o /Users/OK/Downloads/TPP-4.5.1/ trans_proteomic_pipeline/src/../extern/ProteoWizard/pwiz/pwiz/data/ msdata/Serializer_mzXML.cpp g++ -D__LINUX__ -DDEFAULT_TPP_INSTALL_ROOT=\/usr/local/tpp/\ - D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D__INTEL__ -DINLINING - DTPPLIB -fPIC -I. -I/Users/OK/Downloads/TPP-4.5.1/ trans_proteomic_pipeline/src/. -I/Users/OK/Downloads/TPP-4.5.1/ trans_proteomic_pipeline/src/../extern/gzstream -I/Users/OK/Downloads/ TPP-4.5.1/trans_proteomic_pipeline/src/../extern -I/Users/OK/Downloads/ TPP-4.5.1/trans_proteomic_pipeline/src/../build/darwin/ libarchive-2.2.7/libarchive -I/Users/OK/Downloads/TPP-4.5.1/ trans_proteomic_pipeline/src/../build/darwin/expat-2.0.1/lib -I/Users/ OK/Downloads/TPP-4.5.1/trans_proteomic_pipeline/src/../extern/ boost_1_45_0/boost -I/Users/OK/Downloads/TPP-4.5.1/ trans_proteomic_pipeline/src/../extern/boost_1_45_0 -I/Users/OK/ Downloads/TPP-4.5.1/trans_proteomic_pipeline/src/. -I/Users/OK/ Downloads/TPP-4.5.1/trans_proteomic_pipeline/src/../build/darwin/ fann-2.0.0/src/include -I/Users/OK/Downloads/TPP-4.5.1/ trans_proteomic_pipeline/src/../build/darwin/gsl-1.14 -I /opt/local/ include/ -iprefix /Users/OK/Downloads/TPP-4.5.1/ trans_proteomic_pipeline/src/../extern/ProteoWizard/pwiz/ -iwithprefix pwiz/data/msdata -iwithprefix pwiz/data -I/Users/OK/Downloads/ TPP-4.5.1/trans_proteomic_pipeline/src/../extern/ProteoWizard/pwiz - iwithprefix pwiz -iwithprefix pwiz/utility/misc -iwithprefix pwiz/ utility/math -I/Users/OK/Downloads/TPP-4.5.1/trans_proteomic_pipeline/ src/../extern/boost_1_45_0/boost -I/Users/OK/Downloads/TPP-4.5.1/ trans_proteomic_pipeline/src/../extern/boost_1_45_0 -I/Users/OK/ Downloads/TPP-4.5.1/trans_proteomic_pipeline/src/. -iwithprefix libraries/boost_aux -I/Users/OK/Downloads/TPP-4.5.1/ trans_proteomic_pipeline/src/Parsers/ramp -iwithprefix libraries/ libsvm-3.0 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE - DPWIZ_USER_VERSION_INFO_H=\common/TPPVersion.h\ -c -O2 -o /Users/ OK/Downloads/TPP-4.5.1/trans_proteomic_pipeline/src/../build/darwin/ SHA1.pwiz.o /Users/OK/Downloads/TPP-4.5.1/trans_proteomic_pipeline/ src/../extern/ProteoWizard/pwiz/pwiz/utility/misc/SHA1.cpp In file included from /Users/OK/Downloads/TPP-4.5.1/ trans_proteomic_pipeline/src/../extern/ProteoWizard/pwiz/pwiz/utility/ misc/SHA1.cpp:10: /Users/OK/Downloads/TPP-4.5.1/trans_proteomic_pipeline/src/../extern/ ProteoWizard/pwiz/pwiz/utility/misc/endian.hpp:66:2: error: #error Unsupported platform: probably need a platform-specific define above. make: *** [/Users/OK/Downloads/TPP-4.5.1/trans_proteomic_pipeline/ src/../build/darwin/SHA1.pwiz.o] Error 1 Can someone advice? Thanks, Oded -- You received this message because you are subscribed to the Google Groups spctools-discuss group. To post to this group, send email to spctools-discuss@googlegroups.com. To unsubscribe from this group, send email to spctools-discuss+unsubscr...@googlegroups.com
[spctools-discuss] XPRESS discrepancy between ProtXML and PepXML viewers and XPRESS viewer Options
Dear all, I am using TPP for SILAC analysis of Obritrap X!tandem data (with K+8/R +10). I noticed some differences between the peptide Xpress values shown thorough ProtXML viewer (XPressCGIProteinDisplayParser.cgi) and pepXML viewer (PepXMLViewer.cgi) and those that appear in XPressPeptideUpdateParser.cgi (which I assume are the correct ones). These differences are usually not that big (i.e 1-5%) in some cases can be totally off (i.e 0.1 vs 0.25). I have got similar outputs with TPP 4.4.1 on a Mac (OS 10.6) and Win XP. I should mention that I run it all through the gui. Any idea how to overcome it? Many thanks, Oded -- Forwarded message -- From: Jimmy Eng jke...@gmail.com Date: Dec 21 2010, 8:16 am Subject: XPRESS discrepancy between PepXML viewer and XPRESS viewer To: spctools-discuss Oliver, I finally had a chance to revert to 4.3.1 on two machines (linux windows desktop), runXPRESSon an old ICAT dataset, and view the ratios using new 4.4.1 XPressUpdateParser.cgi. On both systems I don't see the inconsistent ratios being reported for this dataset. Then I found some Orbi SILAC datasets which were run under 4.3.1. Viewing the ratios chromatograms using the current 4.4.1 cgi viewer shows the exact same ratios as calculated by 4.3.1XPRESS. At this point, I can't replicate the discrepancy you're seeing. My advice would be to run your analysis again and see if the discrepancy remains. If you still see the problem, isolate a small dataset (single lcms run) and send it to me (mzXML, pep.xml) along with yourXPRESSrun parameters. - Jimmy On Mon, Dec 13, 2010 at 10:02 AM, oschill...@gmail.com oschill...@gmail.com wrote: Sorry for my late reply: the discrepancy occurs when viewing a TPP 4.3 analysis with TPP 4.4. We have now rolled back to TPP 4.3 to keep our XPRESSanalysis consistent. Any advice on how to proceed in the future? Thanks Oliver On Nov 23, 5:46 pm, Jimmy Eng jke...@gmail.com wrote: Oliver, What parameters did you use to runXPRESS? The GUI showing elution profiles has no current support for the isotope option (summed intensities of first N isotope peaks) but otherwise should return the same ratios as that shown in the pepXML file. - Jimmy On Mon, Nov 22, 2010 at 5:09 AM, oschill...@gmail.com oschill...@gmail.com wrote: Dear TPP community, we notice a small discrepancy between theXPRESSvalues displayed in the PepXML viewer tab (table withpeptidesequences etc) and the XPRESStab (graphic display of elution peak). For almost all peptides, we observe slightly differentXPRESSvalues in both tabs. For example, apeptidehas anXPRESSvalue of 2.32:1 in the PepXML viewer and 2.27:1 in theXPRESSviewer. Our impression is that this discrepancy occurs as of TPP 4.4.1 and does not occur for TPP 4.3.x. Can anyone please advice us on how to proceed here? Thanks a lot Oliver -- You received this message because you are subscribed to the Google Groups spctools-discuss group. To post to this group, send email to spctools-discuss@googlegroups.com. To unsubscribe from this group, send email to spctools-discuss+unsubscr...@googlegroups.com. For more options, visit this group athttp://groups.google.com/group/spctools-discuss?hl=en. -- You received this message because you are subscribed to the Google Groups spctools-discuss group. To post to this group, send email to spctools-discuss@googlegroups.com. To unsubscribe from this group, send email to spctools-discuss+unsubscr...@googlegroups.com. For more options, visit this group athttp://groups.google.com/group/spctools-discuss?hl=en. -- You received this message because you are subscribed to the Google Groups spctools-discuss group. To post to this group, send email to spctools-discuss@googlegroups.com. To unsubscribe from this group, send email to spctools-discuss+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
[spctools-discuss] Label-free with XPRESS
Hi, I am trying to test XPRESS label-free option by using the XPRESS -l option and I have struggles parsing the relevant parameters of the pepXML. I wonder if there is any simple solution to do so? In addition I don't see that any of the label free info is incorporated into protXML, is there a way to that too? Are there any plans to include the label-free related options (quantification and visualization) in the GUI. Many thanks, Oded -- You received this message because you are subscribed to the Google Groups spctools-discuss group. To post to this group, send email to spctools-discuss@googlegroups.com. To unsubscribe from this group, send email to spctools-discuss+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
[spctools-discuss] Using fsata.pro files
Hi all, Is there a way to use fasta.pro files (for X!Tandem search) with the TPP? Thanks, Oded -- You received this message because you are subscribed to the Google Groups spctools-discuss group. To post to this group, send email to spctools-disc...@googlegroups.com. To unsubscribe from this group, send email to spctools-discuss+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
[spctools-discuss] PepC (and TPP) Build error on OS 10.5
Hi all, I am trying to install the latest TPP code (version 4984) on my Mac that runs 10.5 using fink. All seems to go well but a Java related issue in the build of PepC is causing the following error: [javac] /Users/oded/tpp4984/src/Quantitation/Pepc/src/ PepcViewer.java:52: cannot find symbol [javac] symbol : class TableRowSorter [javac] location: package javax.swing.table [javac] import javax.swing.table.TableRowSorter; [javac] ^ [javac] /Users/oded/tpp4984/src/Quantitation/Pepc/src/ PepcViewer.java:473: cannot find symbol [javac] symbol : method setAutoCreateRowSorter(boolean) [javac] location: class javax.swing.JTable [javac] proteinsTable.setAutoCreateRowSorter(true); // sort on col header clicks [javac] ^ [javac] /Users/oded/tpp4984/src/Quantitation/Pepc/src/ PepcViewer.java:482: cannot find symbol [javac] symbol : class TableRowSorter [javac] location: class PepcViewer.PepcPanel [javac] ((TableRowSorter)proteinsTable.getRowSorter()).setComparator(c,dcomp); [javac] ^ [javac] /Users/oded/tpp4984/src/Quantitation/Pepc/src/ PepcViewer.java:482: cannot find symbol [javac] symbol : method getRowSorter() [javac] location: class javax.swing.JTable [javac] ((TableRowSorter)proteinsTable.getRowSorter()).setComparator(c,dcomp); [javac] ^ [javac] /Users/oded/tpp4984/src/Quantitation/Pepc/src/ PepcViewer.java:486: cannot find symbol [javac] symbol : class TableRowSorter [javac] location: class PepcViewer.PepcPanel [javac] ((TableRowSorter)proteinsTable.getRowSorter()).setComparator(getGStatisticColumnNum(),dcomp); [javac] ^ [javac] /Users/oded/tpp4984/src/Quantitation/Pepc/src/ PepcViewer.java:486: cannot find symbol [javac] symbol : method getRowSorter() [javac] location: class javax.swing.JTable [javac] ((TableRowSorter)proteinsTable.getRowSorter()).setComparator(getGStatisticColumnNum(),dcomp); [javac] ^ [javac] /Users/oded/tpp4984/src/Quantitation/Pepc/src/ PepcViewer.java:488: cannot find symbol [javac] symbol : class TableRowSorter [javac] location: class PepcViewer.PepcPanel [javac] ((TableRowSorter)proteinsTable.getRowSorter()).setComparator(getPValueColumnNum(), dcomp); [javac] ^ [javac] /Users/oded/tpp4984/src/Quantitation/Pepc/src/ PepcViewer.java:488: cannot find symbol [javac] symbol : method getRowSorter() [javac] location: class javax.swing.JTable [javac] ((TableRowSorter)proteinsTable.getRowSorter()).setComparator(getPValueColumnNum(), dcomp); [javac] ^ [javac] Note: /Users/oded/tpp4984/src/Quantitation/Pepc/src/ PepcViewer.java uses unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [javac] 8 errors BUILD FAILED The Java build is 1.5.0_24-149 (OS 10.5) Is there a way to sort this issue? Many thanks, Oded -- You received this message because you are subscribed to the Google Groups spctools-discuss group. To post to this group, send email to spctools-disc...@googlegroups.com. To unsubscribe from this group, send email to spctools-discuss+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
[spctools-discuss] MS1 quantification improvments?
Hi All, Are there any planned improvements or development of new tools for MS1 quantification. I use Xpress and it work pretty well for me but still require a bit of manual inspection. As for ASAPratio I find it to be usually off and to require a lot (too much) of manual inspection and correction (which is also not too user-friendly but this is a different story). More specificially, it would be great to have the ability for Xpress to calculate the protein ratios following the median of the identified peptides ratio and not the mean (as in MaxQuant). I tried to use Excel for such calculation after exporting ProteinProphet output (while checking the show peptides option) but currently only the mean ratio is being exported and not the specific ratio of each peptide within a protein. Thanks, Oded -- You received this message because you are subscribed to the Google Groups spctools-discuss group. To post to this group, send email to spctools-disc...@googlegroups.com. To unsubscribe from this group, send email to spctools-discuss+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
[spctools-discuss] Re: MS1 quantification improvments?
Thanks Jimmy - that would be great. Oded On Apr 7, 6:24 pm, Jimmy Eng jke...@gmail.com wrote: Sadly the need for manual inspection isn't going to go away soon but things will get better with peak picking. I'll look into adding using median instead of mean as a user option. On Wed, Apr 7, 2010 at 12:44 AM, Oded oded.kleif...@gmail.com wrote: Hi All, Are there any planned improvements or development of new tools for MS1 quantification. I use Xpress and it work pretty well for me but still require a bit of manual inspection. As for ASAPratio I find it to be usually off and to require a lot (too much) of manual inspection and correction (which is also not too user-friendly but this is a different story). More specificially, it would be great to have the ability for Xpress to calculate the protein ratios following the median of the identified peptides ratio and not the mean (as in MaxQuant). I tried to use Excel for such calculation after exporting ProteinProphet output (while checking the show peptides option) but currently only the mean ratio is being exported and not the specific ratio of each peptide within a protein. Thanks, Oded -- You received this message because you are subscribed to the Google Groups spctools-discuss group. To post to this group, send email to spctools-disc...@googlegroups.com. To unsubscribe from this group, send email to spctools-discuss+unsubscr...@googlegroups.com. For more options, visit this group athttp://groups.google.com/group/spctools-discuss?hl=en. -- You received this message because you are subscribed to the Google Groups spctools-discuss group. To post to this group, send email to spctools-disc...@googlegroups.com. To unsubscribe from this group, send email to spctools-discuss+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
[spctools-discuss] Re: RAW to mzXML (and mzXL) problem TPP4.3
Hi , Is it possible to get this bug fix (thanks again Brian) into windows installation package? Thanks, Oded On Aug 17, 9:48 pm, Brian Pratt brian.pr...@insilicos.com wrote: It would be interesting to see the difference between themzXMLfile that worked and the one that didn't. X!Tandem has its ownmzXMLparser and it might need a tweak. Perhaps you could send me those files? Thanks, Brian -Original Message- From: spctools-discuss@googlegroups.com [mailto:spctools-disc...@googlegroups.com] On Behalf OfOded Sent: Saturday, August 15, 2009 1:08 PM To: spctools-discuss Subject: [spctools-discuss] RAW tomzXML(and mzXL) problem TPP4.3 Hi, I'm having problems converting RAW data tomzXMLwith TPP4.3. I tested different files on 2 different WinXP computers installed with TPP4.3. The conversion tomzXMLgoes just fine and the output can be used with Pep3D. However, while trying to run a Tandem search with the TPP4.3-generatedmzXMLfile as input the following error message pop-up: run_in.exe error run_in.exe has encountered a problem and needs to close. We are sorry for the inconvenience. In the detailes section I can see that the error signature is: szAppName : run_in.exe szAppVer : 0.0.0.0 szModName : msvcrt.dll szModVer : 7.0.2600.5512 offset : 00037b26 If I try to use the samemzXMLfor X! Tandem search on a Mac running TPP 4.3 (or 4.2) I'm getting the following message: X! TANDEM 2 (2007.07.01.3) Loading spectra .Unsupported compression type 'none'. Command FAILED I tried to use different conversion options (i.e profile, centroid, with or with out comprssing) but still got the same error messages. In addition conversion to mzXL failed showing the following error message c:\Inetpub\tpp-bin\msconvert -v --mzML -o c:/Inetpub/wwwroot/ISB/data/ Test/Markers -c [1,2] c:/Inetpub/wwwroot/ISB/data/Test/Markers/ LFok08.RAW Unable to read configuration file [1,2] format: mzML (Precision_64 [ 1000514:Precision_64 1000515:Precision_32 ], ByteOrder_LittleEndian, Compression_None) indexed=true outputPath: c:/Inetpub/wwwroot/ISB/data/Test/Markers extension: .mzML contactFilename: filters: filenames: c:/Inetpub/wwwroot/ISB/data/Test/Markers/LFok08.RAW processing file: c:/Inetpub/wwwroot/ISB/data/Test/Markers/LFok08.RAW [MSDataFile::readFile()] Unsupported file format. Error processing file c:/Inetpub/wwwroot/ISB/data/Test/Markers/ LFok08.RAW Converting the same files on TPP4.2 (rev1) generate fully fuctionalmzXMLfiles. Any help would be appreciated,Oded --~--~-~--~~~---~--~~ You received this message because you are subscribed to the Google Groups spctools-discuss group. To post to this group, send email to spctools-discuss@googlegroups.com To unsubscribe from this group, send email to spctools-discuss+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en -~--~~~~--~~--~--~---
[spctools-discuss] Re: RAW to mzXML (and mzXL) problem TPP4.3
Thanks Natalie, On Sep 9, 11:57 pm, Natalie Tasman natalie.tas...@insilicos.com wrote: Hello Oded, Please see the recently released 4.3.1 version of the TPP, which contains the fix that you mention. Best wishes, Natalie On Sep 9, 2009, at 12:49 PM, Oded wrote: Hi , Is it possible to get this bug fix (thanks again Brian) into windows installation package? Thanks, Oded On Aug 17, 9:48 pm, Brian Pratt brian.pr...@insilicos.com wrote: It would be interesting to see the difference between themzXMLfile that worked and the one that didn't. X!Tandem has its ownmzXMLparser and it might need a tweak. Perhaps you could send me those files? Thanks, Brian -Original Message- From: spctools-discuss@googlegroups.com [mailto:spctools-disc...@googlegroups.com] On Behalf OfOded Sent: Saturday, August 15, 2009 1:08 PM To: spctools-discuss Subject: [spctools-discuss] RAW tomzXML(and mzXL) problem TPP4.3 Hi, I'm having problems converting RAW data tomzXMLwith TPP4.3. I tested different files on 2 different WinXP computers installed with TPP4.3. The conversion tomzXMLgoes just fine and the output can be used with Pep3D. However, while trying to run a Tandem search with the TPP4.3- generatedmzXMLfile as input the following error message pop-up: run_in.exe error run_in.exe has encountered a problem and needs to close. We are sorry for the inconvenience. In the detailes section I can see that the error signature is: szAppName : run_in.exe szAppVer : 0.0.0.0 szModName : msvcrt.dll szModVer : 7.0.2600.5512 offset : 00037b26 If I try to use the samemzXMLfor X! Tandem search on a Mac running TPP 4.3 (or 4.2) I'm getting the following message: X! TANDEM 2 (2007.07.01.3) Loading spectra .Unsupported compression type 'none'. Command FAILED I tried to use different conversion options (i.e profile, centroid, with or with out comprssing) but still got the same error messages. In addition conversion to mzXL failed showing the following error message c:\Inetpub\tpp-bin\msconvert -v --mzML -o c:/Inetpub/wwwroot/ISB/ data/ Test/Markers -c [1,2] c:/Inetpub/wwwroot/ISB/data/Test/Markers/ LFok08.RAW Unable to read configuration file [1,2] format: mzML (Precision_64 [ 1000514:Precision_64 1000515:Precision_32 ], ByteOrder_LittleEndian, Compression_None) indexed=true outputPath: c:/Inetpub/wwwroot/ISB/data/Test/Markers extension: .mzML contactFilename: filters: filenames: c:/Inetpub/wwwroot/ISB/data/Test/Markers/LFok08.RAW processing file: c:/Inetpub/wwwroot/ISB/data/Test/Markers/LFok08.RAW [MSDataFile::readFile()] Unsupported file format. Error processing file c:/Inetpub/wwwroot/ISB/data/Test/Markers/ LFok08.RAW Converting the same files on TPP4.2 (rev1) generate fully fuctionalmzXMLfiles. Any help would be appreciated,Oded --~--~-~--~~~---~--~~ You received this message because you are subscribed to the Google Groups spctools-discuss group. To post to this group, send email to spctools-discuss@googlegroups.com To unsubscribe from this group, send email to spctools-discuss+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en -~--~~~~--~~--~--~---
[spctools-discuss] Re: X!Tandem Parameters File
Hi James, I'm sure that what I do is the best way but it work for me pretty well: I make one X!tandem input for every search conditions I use and usually save them with the relevant data in the relevant data folder. You can start with X!tandem sample input file (downloaded form http://www.thegpm.org/TANDEM/api/eg.xml) add to it the k-score plugin settings: (http://tools.proteomecenter.org/wiki/index.php?title=TPP:X! Tandem_and_the_TPP) and your specific changes (Lys C etc). And when you will be asked for the parameter file specify this xml file. It will overrule the default parameter file of the TPP when specified. Good luck, Oded On Jun 14, 2:10 am, James Dowell jadow...@hotmail.com wrote: Hi, I am trying to set-up the TPP to run an X!Tandem search. I've read Jimmy Eng's tutorial on using X!Tandem within the TPP. The problem I'm having is editing the X!Tandem parameters file. Should I be editing the default parameters file (tandem_params) in the parameters folder? Or should I be creating a new parameters file in the data folder? I'm trying to search data that needs the enzyme set to Lys-C and I can't seem to find the protein cleavage input in the default params file. Thanks, James --~--~-~--~~~---~--~~ You received this message because you are subscribed to the Google Groups spctools-discuss group. To post to this group, send email to spctools-discuss@googlegroups.com To unsubscribe from this group, send email to spctools-discuss+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en -~--~~~~--~~--~--~---
[spctools-discuss] iProphet
Hi all, Is there a way to display Mascot or/and X!tandem search scores (ion score/expect) in iProphet.pep.xml? I'm using TPP v4.3 JETSTREAM (unstable dev prerelease) rev 0 on Mac Os X but had the same issue with TPP 4.2.0 on WinXP. In addition what is the proper reference for citing iProphet (if there is one)? Any help would be highly appreciated. Oded --~--~-~--~~~---~--~~ You received this message because you are subscribed to the Google Groups spctools-discuss group. To post to this group, send email to spctools-discuss@googlegroups.com To unsubscribe from this group, send email to spctools-discuss+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en -~--~~~~--~~--~--~---
[spctools-discuss] Re: Problem with XPRESS
Hi Xin, Yes - you describe my suggestion correctly - just pay attention that you'll have 2 different files (and names) for your mzXML,out, pepXML and so on. I don't have full explanation for what you see - only my experience with TPP usage, maybe Jimmy or David can answer form the developers point of view . In any case with my data I don't see a big differences in the number of positive hits that can be quantified (i.e doesn't have mixed type labeling of light N-term and heavy lysine or the other way) achieved by the 2 searches vs the single search but I should also note that use Mascot and X!tandem and not Sequest (as far as I remember there were some posts in this list that the 2 searches are even better) . BTW - I can't see the 2 screen captures you mentioned in your original message. On Apr 23, 7:49 pm, Xin Wei catroy...@gmail.com wrote: Hi Oded, Let me see if I understand you. What I did is I searched Sequest using +28Da on K and n-terminus as fixed modification and +4Da on these two sites as variable modification. So my Sequest .OUT files contains the information of both versions of labeling. Now are you asking me to run the Sequest again, but using +28 and +32 individually in two searches, and generate different .OUT files? Actually I've tried this approach before using Sequest only and it didn't work well with lower number of identifications and maybe higher false positives. I've never used this approach on TPP EXPRESS. Other than this suggestion, could you think of any reason that this problem occurs? I am wondering if there is another way to get over this. Thank you very much for your advice! Xin On Apr 22, 2:08 pm, Oded oded.kleif...@gmail.com wrote: Hi Xin, Try this: Make 2 copies of your mzXML/mzXL file (profile is better in my hands). Run 2 separate searches one for fixed light modification (N-term and K) and one for the fixed heavy modification, using one of mzXML for the light and the other for the heavy. Convert each of the search outputs to pepXML Run peptide prophet on both pepXML and set in the Xpress section Change XPRESS residue mass difference: to the mass difference between the heavy and light (i.e. ~4) for K and for N-term (called n) Good luck, Oded On Apr 21, 9:30 pm, Xin Wei catroy...@gmail.com wrote: Dear all, I just had a problem with the XPRESS quantitation. All the ratios were -1.0 and when I clicked on the ratio, I couldn't see any scans or extracted ion chromatogram. I used formaldehyde labeling on lysine (K) and N-terminus, so it's +28 Da on light label and +32 Da on heavy labels, with 4Da difference. I have uploaded two screen captures of what I described in the Files named XIC and EXPRESS. Has anyone had similar problems before? Your help is greatly appreciated! Xin --~--~-~--~~~---~--~~ You received this message because you are subscribed to the Google Groups spctools-discuss group. To post to this group, send email to spctools-discuss@googlegroups.com To unsubscribe from this group, send email to spctools-discuss+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en -~--~~~~--~~--~--~---
[spctools-discuss] label free quantification with Xpress
Hi all,
About 2 years ago there was a thread about using Xpress to determine
peak area for label free quantification (using the -M option).
{http://groups.google.com/group/spctools-discuss/browse_thread/thread/
4503efcb3de121ae/4d7b98b5a9c6aefc?lnk=gstq=label%2Bfree
%2BXpress#4d7b98b5a9c6aefc}
This work pretty well for me on the peptide level but I wonder if
there is a way to use this data and get info on the protein level
using the TPP (or else). The best thing would be to get this data
somehow into protein prophet but if there is another way that would be
great.
Thanks for any help.
Oded
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[spctools-discuss] Save subset of pepXML to a file
Hi, Long time ago there was an option to save a subset of a pepXML (for example only peptides with ratio 2) to a new pepXML file through the GUI but I haven't seen it for a while. Is it still possible to it with the latest TPP though the GUI (or by using the command line somehow). Thanks for any help. Oded --~--~-~--~~~---~--~~ You received this message because you are subscribed to the Google Groups spctools-discuss group. To post to this group, send email to spctools-discuss@googlegroups.com To unsubscribe from this group, send email to spctools-discuss+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en -~--~~~~--~~--~--~---
[spctools-discuss] Re: re-posting iPROPHET
Hi, Just to add to Ulrich's message: Xpress and ASAPratio values also are not parsed into iProphet.pep.xml and in general it seems that the current viewer not fully adjusted for iProphet output (or maybe the other way around). Like Ulrich, I'm also using iProphet to combine results from different search engines - in the current pepXML output there are 2 probabilities pepP (which seems like the highest PP probability found for duplicated peptides) and iP (which I assume is the one to follow), but I can't see the sensitivity and error curves of either of them and more_pepanal.pl output is just a single line with the location of the iProphet.pep.xml file. I also wonder which of one of the probabilities is used and reported by the Calculate Statistics option. I'm using TPP v4.3 JETSTREAM (unstable dev prerelease) rev 0, Build 200903041031 on Mac with OS 10.5.6 but saw similar output on RPP v4.2 on PC with winXP. Thanks, Oded On Mar 20, 7:50 pm, Ulrich auf dem Keller ukel...@interchange.ubc.ca wrote: Hi Natalie and David, I am using iProphet to combine results from different search engines on the same experiment. It works very well and enhances the number of reliable identifications significantly. Thanks for this piece of software! A minor drawback at the moment is that libra quantification values in iProphet pep.xml files are not .parsed by PepXMLViewer. It would be great if you had time to integrate this option in future releases. Thanks a lot. Cheers, Ulrich On Mar 10, 2009, at 10:06 AM, Alex_PCB wrote: Hi all, I'm re-posting a question on iPROPHET. Here we go: I am trying to run iPROPHET within the latest version of TPP (4.2) and got a little confused with the pipeline. I will try to elaborate a few questions and would appreciate any help. 1) I 've been using TPP for a few months now and my understanding is that I should run iProphet in the xinteract command (something like - ip). However, i don't quite understand which models i should use. For example, i have three technical replicates of a MUDPIT experiments with 20 fractions per replicate. Should I call all my tandem pepxml files from the three experiments within the same xinteract, right?!?!?! Should I enable all models??? 2) There is a -E option to label spectra. How should I use that? 3) What if I want to combine different database search results? Is the procedure similar? I mean, should i use the same models? 4) One more thing, my experiments are iTRAQ labeled. How iProphet would deal with it? Thank you for your time. regards, Alex --~--~-~--~~~---~--~~ You received this message because you are subscribed to the Google Groups spctools-discuss group. To post to this group, send email to spctools-discuss@googlegroups.com To unsubscribe from this group, send email to spctools-discuss+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en -~--~~~~--~~--~--~---
[spctools-discuss] Re: PeptideProphet hangs when initializing stats
Hi, I have seen something similar in some cases but when using X! tandem branch and selecting the option of Use Gamma distribution to model the negatives since this option is unique to X!tandem I don't know if and how this is related to what you obsevered but the outcome and the extact stage are identical. I hope that might help. Oded On Mar 13, 8:34 pm, Dave @ UPENN davejun...@gmail.com wrote: Hey, I've never encountered this before but when i try to run xinteract, peptideprophet hangs during the initializing stats step. i tried fooling around with the settings with no avail. i tried omitting the - Od, adding -l1, and -p0. Any ideas what could be happening here? Thanks! here's the output: $ /opt/tpp/`uname -p`/bin/xinteract -Ninteract.xml -Old -dREV *.xml /opt/tpp/x86_64/bin/xinteract (TPP v4.1 JETSTREAM rev 1, Build 200812051718 (linux)) running: /opt/tpp/x86_64/bin/InteractParser 'interact.xml' 'CGB-001-289U.pep.xml' 'CGB-001-289V.pep.xml' 'CGB-001-289W.pep.xml' 'CGB-001-289Y.pep.xml' 'CGB-001-289Z.pep.xml' 'CGB-001-299A.pep.xml' 'CGB-001-299B.pep.xml' 'CGB-001-299C.pep.xml' 'CGB-001-299D.pep.xml' 'CGB-001-299E.pep.xml' 'CGB-001-299F.pep.xml' 'CGB-001-299U.pep.xml' 'CGB-001-299V.pep.xml' 'CGB-001-299W.pep.xml' 'CGB-001-299X.pep.xml' 'CGB-001-299Y.pep.xml' 'CGB-001-299Z.pep.xml' 'CGB-001-300A.pep.xml' 'CGB-001-300B.pep.xml' 'CGB-001-300C.pep.xml' 'CGB-001-300D.pep.xml' 'CGB-001-300E.pep.xml' 'CGB-001-300F.pep.xml' 'CGB-001-300U.pep.xml' 'CGB-001-300V.pep.xml' 'CGB-001-300W.pep.xml' 'CGB-001-300X.pep.xml' 'CGB-001-300Y.pep.xml' 'CGB-001-301A.pep.xml' 'CGB-001-301B.pep.xml' 'CGB-001-301C.pep.xml' 'CGB-001-301D.pep.xml' 'CGB-001-301E.pep.xml' 'CGB-001-301F.pep.xml' 'CGB-001-301U.pep.xml' 'CGB-001-301V.pep.xml' 'CGB-001-301W.pep.xml' 'CGB-001-301X.pep.xml' 'CGB-001-301Y.pep.xml' 'CGB-001-301Z.pep.xml' 'CGB-002-297A.pep.xml' 'CGB-002-297B.pep.xml' 'CGB-002-297C.pep.xml' 'CGB-002-297D.pep.xml' 'CGB-002-297E.pep.xml' 'CGB-002-297F.pep.xml' 'CGB-002-297U.pep.xml' 'CGB-002-297V.pep.xml' 'CGB-002-297W.pep.xml' 'CGB-002-297X.pep.xml' 'CGB-002-297Y.pep.xml' 'CGB-002-297Z.pep.xml' 'CGB-002-298A.pep.xml' 'CGB-002-298B.pep.xml' 'CGB-002-298C.pep.xml' 'CGB-002-298D.pep.xml' 'CGB-002-298E_080307154954.pep.xml' 'CGB-002-298E.pep.xml' 'CGB-002-298F_080307173448.pep.xml' 'CGB-002-298F.pep.xml' 'interact.xml' -L'7' Skipping file interact.xml, which has the same name as the output file ... file 1: CGB-001-289U.pep.xml file 2: CGB-001-289V.pep.xml file 3: CGB-001-289W.pep.xml file 4: CGB-001-289Y.pep.xml file 5: CGB-001-289Z.pep.xml file 6: CGB-001-299A.pep.xml file 7: CGB-001-299B.pep.xml file 8: CGB-001-299C.pep.xml file 9: CGB-001-299D.pep.xml file 10: CGB-001-299E.pep.xml file 11: CGB-001-299F.pep.xml file 12: CGB-001-299U.pep.xml file 13: CGB-001-299V.pep.xml file 14: CGB-001-299W.pep.xml file 15: CGB-001-299X.pep.xml file 16: CGB-001-299Y.pep.xml file 17: CGB-001-299Z.pep.xml file 18: CGB-001-300A.pep.xml file 19: CGB-001-300B.pep.xml file 20: CGB-001-300C.pep.xml file 21: CGB-001-300D.pep.xml file 22: CGB-001-300E.pep.xml file 23: CGB-001-300F.pep.xml file 24: CGB-001-300U.pep.xml file 25: CGB-001-300V.pep.xml file 26: CGB-001-300W.pep.xml file 27: CGB-001-300X.pep.xml file 28: CGB-001-300Y.pep.xml file 29: CGB-001-301A.pep.xml file 30: CGB-001-301B.pep.xml file 31: CGB-001-301C.pep.xml file 32: CGB-001-301D.pep.xml file 33: CGB-001-301E.pep.xml file 34: CGB-001-301F.pep.xml file 35: CGB-001-301U.pep.xml file 36: CGB-001-301V.pep.xml file 37: CGB-001-301W.pep.xml file 38: CGB-001-301X.pep.xml file 39: CGB-001-301Y.pep.xml file 40: CGB-001-301Z.pep.xml file 41: CGB-002-297A.pep.xml file 42: CGB-002-297B.pep.xml file 43: CGB-002-297C.pep.xml file 44: CGB-002-297D.pep.xml file 45: CGB-002-297E.pep.xml file 46: CGB-002-297F.pep.xml file 47: CGB-002-297U.pep.xml file 48: CGB-002-297V.pep.xml file 49: CGB-002-297W.pep.xml file 50: CGB-002-297X.pep.xml file 51: CGB-002-297Y.pep.xml file 52: CGB-002-297Z.pep.xml file 53: CGB-002-298A.pep.xml file 54: CGB-002-298B.pep.xml file 55: CGB-002-298C.pep.xml file 56: CGB-002-298D.pep.xml file 57: CGB-002-298E_080307154954.pep.xml file 58: CGB-002-298E.pep.xml file 59: CGB-002-298F_080307173448.pep.xml file 60: CGB-002-298F.pep.xml processed altogether 114484 results results written to file /data/www/htdocs/qInteract/data2/ tilo_20081214124503/tilo_3527/interact.shtml command completed in 23 sec running: /opt/tpp/x86_64/bin/PeptideProphetParser 'interact.xml' LEAVE DECOYPROBS DECOY=REV Using Decoy Label REV. Decoy Probabilities will be reported. (SEQUEST) (leaving deltacn* entries) init with SEQUEST trypsin MS Instrument info: Manufacturer: Thermo Scientific, Model: LTQ FT, Ionization: ESI, Analyzer: FTMS, Detector: unknown PeptideProphet (TPP v4.1 JETSTREAM rev 1, Build 200812051718 (linux)) akel
[spctools-discuss] ASAPratio and +5 charge state
Hi, I think there is a problem with ASAPratio calculations for +5 (and higher) charge states - the ratio for many (not all) peptides that where identified with X!tandem at +5 is not calculated and the shown scans scale is usually off and not including the CID (using TPP build 200903041031 on OS X) . Cheers, Oded --~--~-~--~~~---~--~~ You received this message because you are subscribed to the Google Groups spctools-discuss group. To post to this group, send email to spctools-discuss@googlegroups.com To unsubscribe from this group, send email to spctools-discuss+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en -~--~~~~--~~--~--~---
[spctools-discuss] Re: Error using mzXML.gz as input
Hi Brian, Thanks for the quick reply - this fix does solve the search results file name issue but now there are problems with viewing the spectra (using pepXML viewer) which lead to Windows error message saying: plot-msms.cgi has encountered a problem and needs to close. We are sorry for the inconvenience. etc. In the Apache error log I case see the following line if that might help somehow: [Tue Mar 03 11:16:28 2009] [error] [client 127.0.0.1] Use of uninitialized value in -d at C:/Perl/lib/CGI.pm line 4083., referer: http://localhost/tpp-bin/tpp_gui.pl?Action=displaypage=results [Tue Mar 03 11:16:52 2009] [error] [client 127.0.0.1] Premature end of script headers: plot-msms.cgi, referer: http://localhost/ISB/data/OK1/June07/interact.pep.shtml Cheers, Oded On Mar 2, 9:43 pm, Brian Pratt brian.pr...@insilicos.com wrote: Oded, I'm sure you're right in your diagnosis, and thanks for doing the hard part! Try changing this line $out_file =~ s/\.mz[X]?ML$/\.tandem/i; to $out_file =~ s/\.mz[X]?ML(\.gz)?$/\.tandem/i; Please let me know if that works and I'll make the change for the next release. Thanks, Brian -Original Message- From: spctools-discuss@googlegroups.com [mailto:spctools-disc...@googlegroups.com] On Behalf Of Oded Sent: Saturday, February 28, 2009 11:33 AM To: spctools-discuss Subject: [spctools-discuss] Error using mzXML.gz as input Hi all, I'm having problems using the gzipped mzXML files as input (In TPP 4.2 both on OS X and Win). While doing X!Tandem search the results file overwrite the input file and appear under that same name without the .tandem For example the search results of Seq1.mzXML.gz will have the name of Seq1.mzXML.gz and not the name Seq1.tandem or something similar. (look like similar to what happened in 4.1 rev while using mzXL see:http://groups.google.com/group/spctools-discuss/browse_thread/thread/63b 8a308c04aaf3d/1cadb91f3ac730b5?lnk=gstq=mzml#1cadb91f3ac730b5 so I guess it shouldn't be too hard to fix) Cheers, Oded --~--~-~--~~~---~--~~ You received this message because you are subscribed to the Google Groups spctools-discuss group. To post to this group, send email to spctools-discuss@googlegroups.com To unsubscribe from this group, send email to spctools-discuss+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en -~--~~~~--~~--~--~---
[spctools-discuss] Error using mzXML.gz as input
Hi all, I'm having problems using the gzipped mzXML files as input (In TPP 4.2 both on OS X and Win). While doing X!Tandem search the results file overwrite the input file and appear under that same name without the .tandem For example the search results of Seq1.mzXML.gz will have the name of Seq1.mzXML.gz and not the name Seq1.tandem or something similar. (look like similar to what happened in 4.1 rev while using mzXL see:http://groups.google.com/group/spctools-discuss/ browse_thread/thread/63b8a308c04aaf3d/1cadb91f3ac730b5? lnk=gstq=mzml#1cadb91f3ac730b5 so I guess it shouldn't be too hard to fix) Cheers, Oded --~--~-~--~~~---~--~~ You received this message because you are subscribed to the Google Groups spctools-discuss group. To post to this group, send email to spctools-discuss@googlegroups.com To unsubscribe from this group, send email to spctools-discuss+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en -~--~~~~--~~--~--~---
[spctools-discuss] X!tandem parent monoisotopic mass isotope error
Hi all, Following one of the recommendations given here by Alexey for setting X!tandem search parameters (http://groups.google.com/group/spctools- discuss/browse_thread/thread/85609368a910f29d/6e78ce0a43026f2e? lnk=gstq=monoisotopic%2Berror#6e78ce0a43026f2eP) I routinely set the parent monoisotopic mass isotope error option for X!tandem to yes. Usually there ain't too many hits with parent ion shifts but now I have few SILAC datasets that include relatively large numbers of such hits which make me wonder how these hits are actually treated by the TPP: 1)Does these shifts are incorporated somehow into peptide prophet scoring? it seems that although (some of) these hits are getting very high peptide prophet probabilities, they are defined as peptides with large massdiff and their theoretical masses shown in Comet spectrum viewer does not include the parent mass shift. 2)How such peptides are used in Xpress or ASAPratio analysis? from a quick check it seems that the peak area is always calculated for the +1 shift even if the shift is of +2. Thanks, Oded --~--~-~--~~~---~--~~ You received this message because you are subscribed to the Google Groups spctools-discuss group. To post to this group, send email to spctools-discuss@googlegroups.com To unsubscribe from this group, send email to spctools-discuss+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en -~--~~~~--~~--~--~---
[spctools-discuss] Re: ASAPRatio - multi-threading
Hi Walter, The actual performance are of course dependent on the data and analysis but it is possible to use one core and single thread for most of TPP functions. There is a specific issue with ASAPratio that make the calculations rather slow but using the same files and similar analysis with Xpress are much faster (although this is not always possible to switch ASAPratio and Xpress). In any case if you plan your hardware I suggest to aim higher than single core - we use routinely 2 years old dual core intel with 1G RAM and it works just fine (although it would be better to have more RAM). Cheers, Oded On Jan 23, 8:37 am, Walter w.blackst...@gmail.com wrote: Hi, Useful fixes, but the original question seems unanswered. Is it correct that only one core and a single thread are utilised? Is this true for TPP in general? (No criticism implied BTW, just need to plan the hardware). Thanks Walter On Jan 23, 10:43 am, shygza shy...@gmail.com wrote: Kelly, It may be helpful to use ramdisk tool to map your data into your huge RAM, and because TPP web interface can only use files in its root directory, you have to run ASAPRatio in command mode. Chengpin 2009/1/22 Kelly Hogue kelly.ho...@gmail.com Thanks Brian. BTW, my server has 64 GB RAM not 64 MB RAM. Small typo... Is there any chance that ASAPRatio can be written to run the files in parallel? I am sure this is not trivial. Kelly On Fri, Jan 23, 2009 at 3:33 AM, Brian Pratt brian.pr...@insilicos.comwrote: Kelly, Looks like your data FTP'd fine. I'll look into these performance issues, but I note with just a quick eyeballing of the files that you aren't using data compression on the peaklists. This can't be helping since it greatly increases disk IO, which is of course slow. You might try reconverting those files with ReAdW and the –z option (why this isn't the default, I cannot say – I think maybe because X!Tandem didn't used to deal with it, but it does now). Brian -- *From:* spctools-discuss@googlegroups.com [mailto: spctools-disc...@googlegroups.com] *On Behalf Of *Kelly Hogue *Sent:* Wednesday, January 21, 2009 1:09 AM *To:* spctools-discuss@googlegroups.com *Subject:* [spctools-discuss] Re: ASAPRatio - multi-threading I am fairly certain it is ASAPRatio that is the bottleneck but don't quote me on that. Here are the commands from the run so far: # Commands for session DPBYHSST7 on Thu Jan 15 12:19:15 2009 # BEGIN COMMAND BLOCK ## BEGIN Command Execution ## [Thu Jan 15 12:19:15 2009] EXECUTING: run_in c:/Inetpub/wwwroot/ISB/data/G041L10; xinteract -NG041L10_arthur_interact.pep.xml -p0.05 -l7 -x20 -OANp -dREV_ -X-m0.05-nK,8.014199 -A-lK-F-B-r0.05-mK136.109161 c:/Inetpub/wwwroot/ISB/data/G041L10/B_081030_35_G041L10_F11.tandem.pep.xml c:/Inetpub/wwwroot/ISB/data/G041L10/B_081030_36_G041L10_F12.tandem.pep.xml c:/Inetpub/wwwroot/ISB/data/G041L10/B_081030_37_G041L10_G01.tandem.pep.xml c:/Inetpub/wwwroot/ISB/data/G041L10/B_081030_38_G041L10_G02.tandem.pep.xml c:/Inetpub/wwwroot/ISB/data/G041L10/B_081030_39_G041L10_G03.tandem.pep.xml c:/Inetpub/wwwroot/ISB/data/G041L10/B_081030_40_G041L10_G04.tandem.pep.xml c:/Inetpub/wwwroot/ISB/data/G041L10/B_081030_41_G041L10_G05.tandem.pep.xml c:/Inetpub/wwwroot/ISB/data/G041L10/B_081030_42_G041L10_G06.tandem.pep.xml c:/Inetpub/wwwroot/ISB/data/G041L10/B_081030_43_G041L10_G07.tandem.pep.xml c:/Inetpub/wwwroot/ISB/data/G041L10/B_081030_44_G041L10_G08.tandem.pep.xml c:/Inetpub/wwwroot/ISB/data/G041L10/B_081030_45_G041L10_G09.tandem.pep.xml c:/Inetpub/wwwroot/ISB/data/G041L10/B_081030_46_G041L10_G10.tandem.pep.xml c:/Inetpub/wwwroot/ISB/data/G041L10/B_081030_47_G041L10_G11.tandem.pep.xml c:/Inetpub/wwwroot/ISB/data/G041L10/B_081030_48_G041L10_G12.tandem.pep.xml c:/Inetpub/wwwroot/ISB/data/G041L10/B_081030_49_G041L10_H01.tandem.pep.xml c:/Inetpub/wwwroot/ISB/data/G041L10/B_081030_50_G041L10_H02.tandem.pep.xml c:/Inetpub/wwwroot/ISB/data/G041L10/B_081030_51_G041L10_H03.tandem.pep.xml c:/Inetpub/wwwroot/ISB/data/G041L10/B_081030_52_G041L10_H04.tandem.pep.xml c:/Inetpub/wwwroot/ISB/data/G041L10/B_081030_53_G041L10_H05.tandem.pep.xml c:/Inetpub/wwwroot/ISB/data/G041L10/B_081103_51_G041L10_F11_R2.tandem.pep.xml c:/Inetpub/wwwroot/ISB/data/G041L10/B_081103_52_G041L10_F12_R2.tandem.pep.xml c:/Inetpub/wwwroot/ISB/data/G041L10/B_081103_53_G041L10_G01_R2.tandem.pep.xml c:/Inetpub/wwwroot/ISB/data/G041L10/B_081103_54_G041L10_G02_R2.tandem.pep.xml c:/Inetpub/wwwroot/ISB/data/G041L10/B_081103_55_G041L10_G03_R2.tandem.pep.xml c:/Inetpub/wwwroot/ISB/data/G041L10/B_081103_56_G041L10_G04_R2.tandem.pep.xml c:/Inetpub/wwwroot/ISB/data/G041L10/B_081103_57_G041L10_G05_R2.tandem.pep.xml c:/Inetpub/wwwroot/ISB/data/G041L10/B_081103_58_G041L10_G06_R2.tandem.pep.xml c:/Inetpub
[spctools-discuss] Re: TPP 4.1.1 and mzXL
Thank you Natalie and Luis - following your advice and using yesterday release things are working fine now. Cheers, Oded On Nov 17, 8:38 pm, Luis Mendoza [EMAIL PROTECTED] wrote: Hello, 2) Thank you for reporting the tandem/mzML issue. We'll take a look. Ah yes, this is a new change (mzML support in Tandem) that Petunia was not ready for; it still thinks in mzXML terms. Sorry about that. For a quick fix, please open the file C:\Inetpub\tpp-bin\tpp_gui.pl in Wordpad (or Notepad, etc) and change line number 2494 from: $out_file =~ s/\.mzXML$/\.tandem/i; to: $out_file =~ s/\.mz[X]?ML$/\.tandem/i; (add square brackets around the X, followed by a question mark). Save the file, and please try again. We'll include a fix in the next release. Thanks for reporting this! --Luis On Mon, Nov 17, 2008 at 5:29 AM, Oded [EMAIL PROTECTED] wrote: Hi all, [...] In addition, if I use mzXL (that was created using TPP 4.1 ver0), for X!Tandem search the results file overwrite the input file and appear under that same name without the .tandem For example the search results of Seq16480_orbi.mzXL will have the name of Seq16480_orbi.mzXL and not the name Seq16480_orbi.tandem or something similar. This output file seems to be OK if the .tandem is added in the end. Cheers, Oded --~--~-~--~~~---~--~~ You received this message because you are subscribed to the Google Groups spctools-discuss group. To post to this group, send email to spctools-discuss@googlegroups.com To unsubscribe from this group, send email to [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en -~--~~~~--~~--~--~---
[spctools-discuss] Re: TPP 4.1 fail to run X!tandem search
Hi Natalie, I checked it once and it seems to work! I'll keep on testing it and let you know if I found something wrong. Thanks, Oded On Nov 15, 3:55 am, Natalie Tasman [EMAIL PROTECTED] wrote: Oded, I tested your data-- please try again with 4.1.1 and let us know if it's resolved. The 4.1.0 version of tandem.exe was not working. Natalie On Tue, Nov 11, 2008 at 11:14 AM, Brian Pratt [EMAIL PROTECTED]wrote: Hi Oded, We just did a big update to the Tandem code to add mzML support and pick up some other fixes from the LabKey/CPAS team. Perhaps you could shoot me a data set (sufficient files to execute the xtandem command line seen within the TPP GUI). Thanks, Brian -Original Message- From: spctools-discuss@googlegroups.com [mailto:[EMAIL PROTECTED] On Behalf Of Oded Sent: Tuesday, November 11, 2008 10:35 AM To: spctools-discuss Subject: [spctools-discuss] TPP 4.1 fail to run X!tandem search Hi, I'm trying to run X!tandem search with TPP 4.1 on win XP machine and tandem.exe keep crashing during the search with the following info in the Windows error box: szAppName : tandem.exe szAppVer : 0.0.0.0 szModName : tandem.exe szModVer : 0.0.0.0 offset : 001b99d9 I have seen this using both mzXL and mzXML and on 2 different machines. Hope there is a quick solution. Best regards, Oded --~--~-~--~~~---~--~~ You received this message because you are subscribed to the Google Groups spctools-discuss group. To post to this group, send email to spctools-discuss@googlegroups.com To unsubscribe from this group, send email to [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en -~--~~~~--~~--~--~---
[spctools-discuss] TPP 4.1 fail to run X!tandem search
Hi, I'm trying to run X!tandem search with TPP 4.1 on win XP machine and tandem.exe keep crashing during the search with the following info in the Windows error box: szAppName : tandem.exe szAppVer : 0.0.0.0 szModName : tandem.exe szModVer : 0.0.0.0 offset : 001b99d9 I have seen this using both mzXL and mzXML and on 2 different machines. Hope there is a quick solution. Best regards, Oded --~--~-~--~~~---~--~~ You received this message because you are subscribed to the Google Groups spctools-discuss group. To post to this group, send email to spctools-discuss@googlegroups.com To unsubscribe from this group, send email to [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en -~--~~~~--~~--~--~---
