Re: [spctools-discuss] PeptideProphet returns zero probability for all of the X!Tandem search results
Hi David! I played with the fragment mass tolerance but I am still having the issue. However I searched the problematic files with TPP's X!Tandem (instead of GPM's) and it worked perfectly with Peptide Prophet! Is there a linux version of it which I can use on the cluster or is it just usable inside the TPP's GUI? and why do I usually get Internal Server Error when I select Tandem as the pipeline? Many Thanks, Ali On Wednesday, October 12, 2016 at 6:41:55 PM UTC-4, David Shteynberg wrote: > > The TPP is not tested to work with ProteomeDiscoverer pepXML. Sure you > can send me a sample file, but it may take some time to implement support > for this type of data. Comet is open source and easy to use out of the > box. Why don't you try that route? > > -David > > On Wed, Oct 12, 2016 at 3:24 PM, Ali > > wrote: > >> Dear David >> >> Thank you very much! You were right, the problem was with X!Tandem. I >> decided do the searches with Proteome Discoverer. I exported the results to >> pep.xml (from .msf) using PD but now the results don't work with >> PeptideProphet. I can open them in PepXMLViewer but as I said in another >> post just now, I am having problem with processing them with PeptideProphet >> and InteractParser. Do you have experience with these files? I can send you >> a sample of the pepxml files for you. >> >> Sincerely, >> >> Ali >> >> On Wednesday, October 12, 2016 at 6:12:57 PM UTC-4, David Shteynberg >> wrote: >>> >>> Hi Ali, >>> >>> I searched your data with Comet and PeptideProphet got valid PSMs in the >>> analysis that failed to produce correct results from your GPM-version of >>> tandem on the same data. The problem in your dataset is the Tandem >>> search. Attached are the comet parameters I used to search your data. >>> >>> >>> -David >>> >>> >>> >>> On Wed, Oct 5, 2016 at 9:36 PM, Ali wrote: >>> I sent the link to your email. Thank you very much! On Wednesday, October 5, 2016 at 9:21:04 PM UTC-4, David Shteynberg wrote: > > I cannot tell from the search parameters if there is a problem. The > only issue I saw was that you didn't enable isotopic offsets, which are > sometimes helpful. If you send me a sample mzML file and possibly the > search results in pep.xml along with the database I can troubleshoot > further. One question, you said you are selecting 2+ 3+ and 4+, why are > only 2+ and 3+ in this dataset? Does any other dataset in your analysis > contain 4+? > > -David > > On Wed, Oct 5, 2016 at 6:16 PM, Ali wrote: > >> Hi David >> >> We are only collecting 2+, 3+ and 4+ data. I am working on the >> cluster, so I am using the GPM version and we were unable to install the >> k-score plugin therefore I am using the X! Tandem native scoring for the >> searches. >> >> If you mean combining all of the search results with xinteract and >> then using PeptideProphet (as you instructed), I have not yet done so >> because I wanted to make sure that we are getting results from the >> individual searches. Is there an issue in my search parameters which is >> responsible for the problem? >> >> Many Thanks, >> Ali >> >> On Wednesday, October 5, 2016 at 7:06:19 PM UTC-4, David Shteynberg >> wrote: >>> >>> Hi Ali, >>> >>> >>> Are you setting your instrument to collect only 2+ and 3+ data? Are >>> you using the tandem bundled with TPP or the GPM version of tandem? >>> Have >>> you tried to process all your runs in one file? >>> >>> Thanks, >>> -David >>> >>> >>> On Wed, Oct 5, 2016 at 11:39 AM, Ali wrote: >>> Thank you very much! I really appreciate it! On Tuesday, October 4, 2016 at 8:03:27 PM UTC-4, David Shteynberg wrote: > > PeptideProphet is doing it's job here by telling you that there is > no distinct population of correct results in this search. I suspect > your > search parameters are the problem. This is orbitrap data so the > charges > should be known, but it seems Tandem only searched 2+ and 3+ for you, > this > is somewhat troubling. Tomorrow, I will check your parameters more > carefully to try to identify the actual problem with your search. > > -David > > > On Tue, Oct 4, 2016 at 2:12 PM, Ali wrote: > >> It appears that PeptideProphet fails, I am getting this message: >> >> using Accurate Mass Bins >> using PPM mass difference >> (X! Tandem) (minprob 0) >> adding Accurate Mass mixture distr >> init with X! Tandem trypsin >> MS Instrument info: Manufacturer: Thermo Scientific, Model: >> UNKNOWN, Ionization: nanoelectrospray, Analyzer: orbitrap, Detector: >> inductive detect
Re: [spctools-discuss] PeptideProphet returns zero probability for all of the X!Tandem search results
Thanks David! Let me try lowering fragment mass error. I will let you know about the outcome. Well, we already had the Proteome Discoverer results and we really want to create the spectral library asap, so I was given those results to use instead of X!Tandem. and I have never worked with comet. I have to figure out how it works first. I will upload the ProteomeDiscoverer pep.xml in the folder that you have it's link, if you had a few minutes just take a look at it. May be it needed a few tweaks to work with PeptideProphet. Thanks so much, Ali On Wednesday, October 12, 2016 at 6:41:55 PM UTC-4, David Shteynberg wrote: > > The TPP is not tested to work with ProteomeDiscoverer pepXML. Sure you > can send me a sample file, but it may take some time to implement support > for this type of data. Comet is open source and easy to use out of the > box. Why don't you try that route? > > -David > > On Wed, Oct 12, 2016 at 3:24 PM, Ali > > wrote: > >> Dear David >> >> Thank you very much! You were right, the problem was with X!Tandem. I >> decided do the searches with Proteome Discoverer. I exported the results to >> pep.xml (from .msf) using PD but now the results don't work with >> PeptideProphet. I can open them in PepXMLViewer but as I said in another >> post just now, I am having problem with processing them with PeptideProphet >> and InteractParser. Do you have experience with these files? I can send you >> a sample of the pepxml files for you. >> >> Sincerely, >> >> Ali >> >> On Wednesday, October 12, 2016 at 6:12:57 PM UTC-4, David Shteynberg >> wrote: >>> >>> Hi Ali, >>> >>> I searched your data with Comet and PeptideProphet got valid PSMs in the >>> analysis that failed to produce correct results from your GPM-version of >>> tandem on the same data. The problem in your dataset is the Tandem >>> search. Attached are the comet parameters I used to search your data. >>> >>> >>> -David >>> >>> >>> >>> On Wed, Oct 5, 2016 at 9:36 PM, Ali wrote: >>> I sent the link to your email. Thank you very much! On Wednesday, October 5, 2016 at 9:21:04 PM UTC-4, David Shteynberg wrote: > > I cannot tell from the search parameters if there is a problem. The > only issue I saw was that you didn't enable isotopic offsets, which are > sometimes helpful. If you send me a sample mzML file and possibly the > search results in pep.xml along with the database I can troubleshoot > further. One question, you said you are selecting 2+ 3+ and 4+, why are > only 2+ and 3+ in this dataset? Does any other dataset in your analysis > contain 4+? > > -David > > On Wed, Oct 5, 2016 at 6:16 PM, Ali wrote: > >> Hi David >> >> We are only collecting 2+, 3+ and 4+ data. I am working on the >> cluster, so I am using the GPM version and we were unable to install the >> k-score plugin therefore I am using the X! Tandem native scoring for the >> searches. >> >> If you mean combining all of the search results with xinteract and >> then using PeptideProphet (as you instructed), I have not yet done so >> because I wanted to make sure that we are getting results from the >> individual searches. Is there an issue in my search parameters which is >> responsible for the problem? >> >> Many Thanks, >> Ali >> >> On Wednesday, October 5, 2016 at 7:06:19 PM UTC-4, David Shteynberg >> wrote: >>> >>> Hi Ali, >>> >>> >>> Are you setting your instrument to collect only 2+ and 3+ data? Are >>> you using the tandem bundled with TPP or the GPM version of tandem? >>> Have >>> you tried to process all your runs in one file? >>> >>> Thanks, >>> -David >>> >>> >>> On Wed, Oct 5, 2016 at 11:39 AM, Ali wrote: >>> Thank you very much! I really appreciate it! On Tuesday, October 4, 2016 at 8:03:27 PM UTC-4, David Shteynberg wrote: > > PeptideProphet is doing it's job here by telling you that there is > no distinct population of correct results in this search. I suspect > your > search parameters are the problem. This is orbitrap data so the > charges > should be known, but it seems Tandem only searched 2+ and 3+ for you, > this > is somewhat troubling. Tomorrow, I will check your parameters more > carefully to try to identify the actual problem with your search. > > -David > > > On Tue, Oct 4, 2016 at 2:12 PM, Ali wrote: > >> It appears that PeptideProphet fails, I am getting this message: >> >> using Accurate Mass Bins >> using PPM mass difference >> (X! Tandem) (minprob 0) >> adding Accurate Mass mixture distr >> init with X! Tandem trypsin >> MS Instrument info: Manufacturer: T
Re: [spctools-discuss] PeptideProphet returns zero probability for all of the X!Tandem search results
The TPP is not tested to work with ProteomeDiscoverer pepXML. Sure you can send me a sample file, but it may take some time to implement support for this type of data. Comet is open source and easy to use out of the box. Why don't you try that route? -David On Wed, Oct 12, 2016 at 3:24 PM, Ali wrote: > Dear David > > Thank you very much! You were right, the problem was with X!Tandem. I > decided do the searches with Proteome Discoverer. I exported the results to > pep.xml (from .msf) using PD but now the results don't work with > PeptideProphet. I can open them in PepXMLViewer but as I said in another > post just now, I am having problem with processing them with PeptideProphet > and InteractParser. Do you have experience with these files? I can send you > a sample of the pepxml files for you. > > Sincerely, > > Ali > > On Wednesday, October 12, 2016 at 6:12:57 PM UTC-4, David Shteynberg wrote: >> >> Hi Ali, >> >> I searched your data with Comet and PeptideProphet got valid PSMs in the >> analysis that failed to produce correct results from your GPM-version of >> tandem on the same data. The problem in your dataset is the Tandem >> search. Attached are the comet parameters I used to search your data. >> >> >> -David >> >> >> >> On Wed, Oct 5, 2016 at 9:36 PM, Ali wrote: >> >>> I sent the link to your email. Thank you very much! >>> >>> On Wednesday, October 5, 2016 at 9:21:04 PM UTC-4, David Shteynberg >>> wrote: I cannot tell from the search parameters if there is a problem. The only issue I saw was that you didn't enable isotopic offsets, which are sometimes helpful. If you send me a sample mzML file and possibly the search results in pep.xml along with the database I can troubleshoot further. One question, you said you are selecting 2+ 3+ and 4+, why are only 2+ and 3+ in this dataset? Does any other dataset in your analysis contain 4+? -David On Wed, Oct 5, 2016 at 6:16 PM, Ali wrote: > Hi David > > We are only collecting 2+, 3+ and 4+ data. I am working on the > cluster, so I am using the GPM version and we were unable to install the > k-score plugin therefore I am using the X! Tandem native scoring for the > searches. > > If you mean combining all of the search results with xinteract and > then using PeptideProphet (as you instructed), I have not yet done so > because I wanted to make sure that we are getting results from the > individual searches. Is there an issue in my search parameters which is > responsible for the problem? > > Many Thanks, > Ali > > On Wednesday, October 5, 2016 at 7:06:19 PM UTC-4, David Shteynberg > wrote: >> >> Hi Ali, >> >> >> Are you setting your instrument to collect only 2+ and 3+ data? Are >> you using the tandem bundled with TPP or the GPM version of tandem? Have >> you tried to process all your runs in one file? >> >> Thanks, >> -David >> >> >> On Wed, Oct 5, 2016 at 11:39 AM, Ali wrote: >> >>> Thank you very much! I really appreciate it! >>> >>> On Tuesday, October 4, 2016 at 8:03:27 PM UTC-4, David Shteynberg >>> wrote: PeptideProphet is doing it's job here by telling you that there is no distinct population of correct results in this search. I suspect your search parameters are the problem. This is orbitrap data so the charges should be known, but it seems Tandem only searched 2+ and 3+ for you, this is somewhat troubling. Tomorrow, I will check your parameters more carefully to try to identify the actual problem with your search. -David On Tue, Oct 4, 2016 at 2:12 PM, Ali wrote: > It appears that PeptideProphet fails, I am getting this message: > > using Accurate Mass Bins > using PPM mass difference > (X! Tandem) (minprob 0) > adding Accurate Mass mixture distr > init with X! Tandem trypsin > MS Instrument info: Manufacturer: Thermo Scientific, Model: > UNKNOWN, Ionization: nanoelectrospray, Analyzer: orbitrap, Detector: > inductive detector > > PeptideProphet (TPP v4.8.0 PHILAE, Build 201608051257-exported > (RedHatEnterpriseServer-x86_64)) AKeller@ISB > read in 0 1+, 14418 2+, 11080 3+, 0 4+, 0 5+, 0 6+, and 0 7+ > spectra. > Initialising statistical models ... > negmean = 0.0533258 > negmean = 1 > negmean = 0.0376944 > negmean = -0.2 > negmean = -0.2 > negmean = -0.2 > negmean = -0.2 > Iterations: .10.20. > WARNING: Mixture model quality test failed for charge (2+). > WARNING: Mixture model quality test failed for charge (3+). > > On Monday, October
Re: [spctools-discuss] PeptideProphet returns zero probability for all of the X!Tandem search results
Dear David Thank you very much! You were right, the problem was with X!Tandem. I decided do the searches with Proteome Discoverer. I exported the results to pep.xml (from .msf) using PD but now the results don't work with PeptideProphet. I can open them in PepXMLViewer but as I said in another post just now, I am having problem with processing them with PeptideProphet and InteractParser. Do you have experience with these files? I can send you a sample of the pepxml files for you. Sincerely, Ali On Wednesday, October 12, 2016 at 6:12:57 PM UTC-4, David Shteynberg wrote: > > Hi Ali, > > I searched your data with Comet and PeptideProphet got valid PSMs in the > analysis that failed to produce correct results from your GPM-version of > tandem on the same data. The problem in your dataset is the Tandem > search. Attached are the comet parameters I used to search your data. > > > -David > > > > On Wed, Oct 5, 2016 at 9:36 PM, Ali > > wrote: > >> I sent the link to your email. Thank you very much! >> >> On Wednesday, October 5, 2016 at 9:21:04 PM UTC-4, David Shteynberg wrote: >>> >>> I cannot tell from the search parameters if there is a problem. The >>> only issue I saw was that you didn't enable isotopic offsets, which are >>> sometimes helpful. If you send me a sample mzML file and possibly the >>> search results in pep.xml along with the database I can troubleshoot >>> further. One question, you said you are selecting 2+ 3+ and 4+, why are >>> only 2+ and 3+ in this dataset? Does any other dataset in your analysis >>> contain 4+? >>> >>> -David >>> >>> On Wed, Oct 5, 2016 at 6:16 PM, Ali wrote: >>> Hi David We are only collecting 2+, 3+ and 4+ data. I am working on the cluster, so I am using the GPM version and we were unable to install the k-score plugin therefore I am using the X! Tandem native scoring for the searches. If you mean combining all of the search results with xinteract and then using PeptideProphet (as you instructed), I have not yet done so because I wanted to make sure that we are getting results from the individual searches. Is there an issue in my search parameters which is responsible for the problem? Many Thanks, Ali On Wednesday, October 5, 2016 at 7:06:19 PM UTC-4, David Shteynberg wrote: > > Hi Ali, > > > Are you setting your instrument to collect only 2+ and 3+ data? Are > you using the tandem bundled with TPP or the GPM version of tandem? Have > you tried to process all your runs in one file? > > Thanks, > -David > > > On Wed, Oct 5, 2016 at 11:39 AM, Ali wrote: > >> Thank you very much! I really appreciate it! >> >> On Tuesday, October 4, 2016 at 8:03:27 PM UTC-4, David Shteynberg >> wrote: >>> >>> PeptideProphet is doing it's job here by telling you that there is >>> no distinct population of correct results in this search. I suspect >>> your >>> search parameters are the problem. This is orbitrap data so the >>> charges >>> should be known, but it seems Tandem only searched 2+ and 3+ for you, >>> this >>> is somewhat troubling. Tomorrow, I will check your parameters more >>> carefully to try to identify the actual problem with your search. >>> >>> -David >>> >>> >>> On Tue, Oct 4, 2016 at 2:12 PM, Ali wrote: >>> It appears that PeptideProphet fails, I am getting this message: using Accurate Mass Bins using PPM mass difference (X! Tandem) (minprob 0) adding Accurate Mass mixture distr init with X! Tandem trypsin MS Instrument info: Manufacturer: Thermo Scientific, Model: UNKNOWN, Ionization: nanoelectrospray, Analyzer: orbitrap, Detector: inductive detector PeptideProphet (TPP v4.8.0 PHILAE, Build 201608051257-exported (RedHatEnterpriseServer-x86_64)) AKeller@ISB read in 0 1+, 14418 2+, 11080 3+, 0 4+, 0 5+, 0 6+, and 0 7+ spectra. Initialising statistical models ... negmean = 0.0533258 negmean = 1 negmean = 0.0376944 negmean = -0.2 negmean = -0.2 negmean = -0.2 negmean = -0.2 Iterations: .10.20. WARNING: Mixture model quality test failed for charge (2+). WARNING: Mixture model quality test failed for charge (3+). On Monday, October 3, 2016 at 5:57:39 PM UTC-4, David Shteynberg wrote: > > I highly recommend you start employing decoys in your search > databases. I noticed you are not combining together the runs in the > analysis. If the data was generated and searched in the same way it > should > be analysed together for better statistical power. I suggest you > co
Re: [spctools-discuss] PeptideProphet returns zero probability for all of the X!Tandem search results
My suspicion regarding the Tandem failure is the fragment mass tolerance. I am observing fragment mass differences of much less than 0.05 daltons, yet your Tandem search uses 0.5 daltons as the tolerance. Could GPM-tandem be having a problem there? Can you try to lower the fragment mass tolerance and redo the search? Can you employ comet in your pipeline? -David On Wed, Oct 12, 2016 at 3:12 PM, David Shteynberg < david.shteynb...@systemsbiology.org> wrote: > Hi Ali, > > I searched your data with Comet and PeptideProphet got valid PSMs in the > analysis that failed to produce correct results from your GPM-version of > tandem on the same data. The problem in your dataset is the Tandem > search. Attached are the comet parameters I used to search your data. > > > -David > > > > On Wed, Oct 5, 2016 at 9:36 PM, Ali wrote: > >> I sent the link to your email. Thank you very much! >> >> On Wednesday, October 5, 2016 at 9:21:04 PM UTC-4, David Shteynberg wrote: >>> >>> I cannot tell from the search parameters if there is a problem. The >>> only issue I saw was that you didn't enable isotopic offsets, which are >>> sometimes helpful. If you send me a sample mzML file and possibly the >>> search results in pep.xml along with the database I can troubleshoot >>> further. One question, you said you are selecting 2+ 3+ and 4+, why are >>> only 2+ and 3+ in this dataset? Does any other dataset in your analysis >>> contain 4+? >>> >>> -David >>> >>> On Wed, Oct 5, 2016 at 6:16 PM, Ali wrote: >>> Hi David We are only collecting 2+, 3+ and 4+ data. I am working on the cluster, so I am using the GPM version and we were unable to install the k-score plugin therefore I am using the X! Tandem native scoring for the searches. If you mean combining all of the search results with xinteract and then using PeptideProphet (as you instructed), I have not yet done so because I wanted to make sure that we are getting results from the individual searches. Is there an issue in my search parameters which is responsible for the problem? Many Thanks, Ali On Wednesday, October 5, 2016 at 7:06:19 PM UTC-4, David Shteynberg wrote: > > Hi Ali, > > > Are you setting your instrument to collect only 2+ and 3+ data? Are > you using the tandem bundled with TPP or the GPM version of tandem? Have > you tried to process all your runs in one file? > > Thanks, > -David > > > On Wed, Oct 5, 2016 at 11:39 AM, Ali wrote: > >> Thank you very much! I really appreciate it! >> >> On Tuesday, October 4, 2016 at 8:03:27 PM UTC-4, David Shteynberg >> wrote: >>> >>> PeptideProphet is doing it's job here by telling you that there is >>> no distinct population of correct results in this search. I suspect >>> your >>> search parameters are the problem. This is orbitrap data so the charges >>> should be known, but it seems Tandem only searched 2+ and 3+ for you, >>> this >>> is somewhat troubling. Tomorrow, I will check your parameters more >>> carefully to try to identify the actual problem with your search. >>> >>> -David >>> >>> >>> On Tue, Oct 4, 2016 at 2:12 PM, Ali wrote: >>> It appears that PeptideProphet fails, I am getting this message: using Accurate Mass Bins using PPM mass difference (X! Tandem) (minprob 0) adding Accurate Mass mixture distr init with X! Tandem trypsin MS Instrument info: Manufacturer: Thermo Scientific, Model: UNKNOWN, Ionization: nanoelectrospray, Analyzer: orbitrap, Detector: inductive detector PeptideProphet (TPP v4.8.0 PHILAE, Build 201608051257-exported (RedHatEnterpriseServer-x86_64)) AKeller@ISB read in 0 1+, 14418 2+, 11080 3+, 0 4+, 0 5+, 0 6+, and 0 7+ spectra. Initialising statistical models ... negmean = 0.0533258 negmean = 1 negmean = 0.0376944 negmean = -0.2 negmean = -0.2 negmean = -0.2 negmean = -0.2 Iterations: .10.20. WARNING: Mixture model quality test failed for charge (2+). WARNING: Mixture model quality test failed for charge (3+). On Monday, October 3, 2016 at 5:57:39 PM UTC-4, David Shteynberg wrote: > > I highly recommend you start employing decoys in your search > databases. I noticed you are not combining together the runs in the > analysis. If the data was generated and searched in the same way it > should > be analysed together for better statistical power. I suggest you > combine > the results from all your runs and filter by the spectrum names > later. Try > this: > > InteractParser ./ALL.interact.
Re: [spctools-discuss] PeptideProphet returns zero probability for all of the X!Tandem search results
Hi Ali, I searched your data with Comet and PeptideProphet got valid PSMs in the analysis that failed to produce correct results from your GPM-version of tandem on the same data. The problem in your dataset is the Tandem search. Attached are the comet parameters I used to search your data. -David On Wed, Oct 5, 2016 at 9:36 PM, Ali wrote: > I sent the link to your email. Thank you very much! > > On Wednesday, October 5, 2016 at 9:21:04 PM UTC-4, David Shteynberg wrote: >> >> I cannot tell from the search parameters if there is a problem. The only >> issue I saw was that you didn't enable isotopic offsets, which are >> sometimes helpful. If you send me a sample mzML file and possibly the >> search results in pep.xml along with the database I can troubleshoot >> further. One question, you said you are selecting 2+ 3+ and 4+, why are >> only 2+ and 3+ in this dataset? Does any other dataset in your analysis >> contain 4+? >> >> -David >> >> On Wed, Oct 5, 2016 at 6:16 PM, Ali wrote: >> >>> Hi David >>> >>> We are only collecting 2+, 3+ and 4+ data. I am working on the cluster, >>> so I am using the GPM version and we were unable to install the k-score >>> plugin therefore I am using the X! Tandem native scoring for the searches. >>> >>> If you mean combining all of the search results with xinteract and then >>> using PeptideProphet (as you instructed), I have not yet done so because I >>> wanted to make sure that we are getting results from the individual >>> searches. Is there an issue in my search parameters which is responsible >>> for the problem? >>> >>> Many Thanks, >>> Ali >>> >>> On Wednesday, October 5, 2016 at 7:06:19 PM UTC-4, David Shteynberg >>> wrote: Hi Ali, Are you setting your instrument to collect only 2+ and 3+ data? Are you using the tandem bundled with TPP or the GPM version of tandem? Have you tried to process all your runs in one file? Thanks, -David On Wed, Oct 5, 2016 at 11:39 AM, Ali wrote: > Thank you very much! I really appreciate it! > > On Tuesday, October 4, 2016 at 8:03:27 PM UTC-4, David Shteynberg > wrote: >> >> PeptideProphet is doing it's job here by telling you that there is no >> distinct population of correct results in this search. I suspect your >> search parameters are the problem. This is orbitrap data so the charges >> should be known, but it seems Tandem only searched 2+ and 3+ for you, >> this >> is somewhat troubling. Tomorrow, I will check your parameters more >> carefully to try to identify the actual problem with your search. >> >> -David >> >> >> On Tue, Oct 4, 2016 at 2:12 PM, Ali wrote: >> >>> It appears that PeptideProphet fails, I am getting this message: >>> >>> using Accurate Mass Bins >>> using PPM mass difference >>> (X! Tandem) (minprob 0) >>> adding Accurate Mass mixture distr >>> init with X! Tandem trypsin >>> MS Instrument info: Manufacturer: Thermo Scientific, Model: UNKNOWN, >>> Ionization: nanoelectrospray, Analyzer: orbitrap, Detector: inductive >>> detector >>> >>> PeptideProphet (TPP v4.8.0 PHILAE, Build 201608051257-exported >>> (RedHatEnterpriseServer-x86_64)) AKeller@ISB >>> read in 0 1+, 14418 2+, 11080 3+, 0 4+, 0 5+, 0 6+, and 0 7+ >>> spectra. >>> Initialising statistical models ... >>> negmean = 0.0533258 >>> negmean = 1 >>> negmean = 0.0376944 >>> negmean = -0.2 >>> negmean = -0.2 >>> negmean = -0.2 >>> negmean = -0.2 >>> Iterations: .10.20. >>> WARNING: Mixture model quality test failed for charge (2+). >>> WARNING: Mixture model quality test failed for charge (3+). >>> >>> On Monday, October 3, 2016 at 5:57:39 PM UTC-4, David Shteynberg >>> wrote: I highly recommend you start employing decoys in your search databases. I noticed you are not combining together the runs in the analysis. If the data was generated and searched in the same way it should be analysed together for better statistical power. I suggest you combine the results from all your runs and filter by the spectrum names later. Try this: InteractParser ./ALL.interact.xml ./*.tandem.pep.xml -S -Etrypsin PeptideProphetParser ./ALL.interact.xml ACCMASS PPM NOICAT MINPROB=0 -David On Mon, Oct 3, 2016 at 2:39 PM, Ali wrote: > Hi David > > Thanks for your reply. I don't think so, it is not just one set, > as I said almost a third of my search results are returned with zero > probabilities. All of the searches are done with the same setting and > using > the same database. The fact that for some of the searched files I am > getting zero pr
Re: [spctools-discuss] PeptideProphet returns zero probability for all of the X!Tandem search results
I sent the link to your email. Thank you very much! On Wednesday, October 5, 2016 at 9:21:04 PM UTC-4, David Shteynberg wrote: > > I cannot tell from the search parameters if there is a problem. The only > issue I saw was that you didn't enable isotopic offsets, which are > sometimes helpful. If you send me a sample mzML file and possibly the > search results in pep.xml along with the database I can troubleshoot > further. One question, you said you are selecting 2+ 3+ and 4+, why are > only 2+ and 3+ in this dataset? Does any other dataset in your analysis > contain 4+? > > -David > > On Wed, Oct 5, 2016 at 6:16 PM, Ali > > wrote: > >> Hi David >> >> We are only collecting 2+, 3+ and 4+ data. I am working on the cluster, >> so I am using the GPM version and we were unable to install the k-score >> plugin therefore I am using the X! Tandem native scoring for the searches. >> >> If you mean combining all of the search results with xinteract and then >> using PeptideProphet (as you instructed), I have not yet done so because I >> wanted to make sure that we are getting results from the individual >> searches. Is there an issue in my search parameters which is responsible >> for the problem? >> >> Many Thanks, >> Ali >> >> On Wednesday, October 5, 2016 at 7:06:19 PM UTC-4, David Shteynberg wrote: >>> >>> Hi Ali, >>> >>> >>> Are you setting your instrument to collect only 2+ and 3+ data? Are you >>> using the tandem bundled with TPP or the GPM version of tandem? Have you >>> tried to process all your runs in one file? >>> >>> Thanks, >>> -David >>> >>> >>> On Wed, Oct 5, 2016 at 11:39 AM, Ali wrote: >>> Thank you very much! I really appreciate it! On Tuesday, October 4, 2016 at 8:03:27 PM UTC-4, David Shteynberg wrote: > > PeptideProphet is doing it's job here by telling you that there is no > distinct population of correct results in this search. I suspect your > search parameters are the problem. This is orbitrap data so the charges > should be known, but it seems Tandem only searched 2+ and 3+ for you, > this > is somewhat troubling. Tomorrow, I will check your parameters more > carefully to try to identify the actual problem with your search. > > -David > > > On Tue, Oct 4, 2016 at 2:12 PM, Ali wrote: > >> It appears that PeptideProphet fails, I am getting this message: >> >> using Accurate Mass Bins >> using PPM mass difference >> (X! Tandem) (minprob 0) >> adding Accurate Mass mixture distr >> init with X! Tandem trypsin >> MS Instrument info: Manufacturer: Thermo Scientific, Model: UNKNOWN, >> Ionization: nanoelectrospray, Analyzer: orbitrap, Detector: inductive >> detector >> >> PeptideProphet (TPP v4.8.0 PHILAE, Build 201608051257-exported >> (RedHatEnterpriseServer-x86_64)) AKeller@ISB >> read in 0 1+, 14418 2+, 11080 3+, 0 4+, 0 5+, 0 6+, and 0 7+ spectra. >> Initialising statistical models ... >> negmean = 0.0533258 >> negmean = 1 >> negmean = 0.0376944 >> negmean = -0.2 >> negmean = -0.2 >> negmean = -0.2 >> negmean = -0.2 >> Iterations: .10.20. >> WARNING: Mixture model quality test failed for charge (2+). >> WARNING: Mixture model quality test failed for charge (3+). >> >> On Monday, October 3, 2016 at 5:57:39 PM UTC-4, David Shteynberg >> wrote: >>> >>> I highly recommend you start employing decoys in your search >>> databases. I noticed you are not combining together the runs in the >>> analysis. If the data was generated and searched in the same way it >>> should >>> be analysed together for better statistical power. I suggest you >>> combine >>> the results from all your runs and filter by the spectrum names later. >>> Try >>> this: >>> >>> InteractParser ./ALL.interact.xml ./*.tandem.pep.xml -S -Etrypsin >>> PeptideProphetParser ./ALL.interact.xml ACCMASS PPM NOICAT MINPROB=0 >>> >>> >>> -David >>> >>> On Mon, Oct 3, 2016 at 2:39 PM, Ali wrote: >>> Hi David Thanks for your reply. I don't think so, it is not just one set, as I said almost a third of my search results are returned with zero probabilities. All of the searches are done with the same setting and using the same database. The fact that for some of the searched files I am getting zero probabilities and some of them are just fine is a bit strange. I don't have decoys in my data base. If it helps, I can send you one of the search results with or without PeptideProphet probabilities. Sincerely, Ali On Monday, October 3, 2016 at 4:19:05 PM UTC-4, David Shteynberg wrote: > > Is it possible there are no corr
Re: [spctools-discuss] PeptideProphet returns zero probability for all of the X!Tandem search results
How can I send you these files? Can I upload them on the cloud and send you the link? I am not doing the mass spec so I don't know the details of each experiments but some of them have all three charges and some of them only have 2+ and 3+. Here is an example of similar issue for a file with three charges: PeptideProphet (TPP v4.8.0 PHILAE, Build 201608051257-exported (RedHatEnterpriseServer-x86_64)) AKeller@ISB read in 0 1+, 5857 2+, 2812 3+, 406 4+, 0 5+, 0 6+, and 0 7+ spectra. negmean = 0.0533258 negmean = 1 negmean = 0.901666 negmean = -0.2 negmean = -0.2 negmean = -0.2 negmean = -0.2 WARNING: Mixture model quality test failed for charge (2+). WARNING: Mixture model quality test failed for charge (3+). WARNING: Mixture model quality test failed for charge (4+). Thanks, Ali On Wednesday, October 5, 2016 at 9:21:04 PM UTC-4, David Shteynberg wrote: > > I cannot tell from the search parameters if there is a problem. The only > issue I saw was that you didn't enable isotopic offsets, which are > sometimes helpful. If you send me a sample mzML file and possibly the > search results in pep.xml along with the database I can troubleshoot > further. One question, you said you are selecting 2+ 3+ and 4+, why are > only 2+ and 3+ in this dataset? Does any other dataset in your analysis > contain 4+? > > -David > > On Wed, Oct 5, 2016 at 6:16 PM, Ali > > wrote: > >> Hi David >> >> We are only collecting 2+, 3+ and 4+ data. I am working on the cluster, >> so I am using the GPM version and we were unable to install the k-score >> plugin therefore I am using the X! Tandem native scoring for the searches. >> >> If you mean combining all of the search results with xinteract and then >> using PeptideProphet (as you instructed), I have not yet done so because I >> wanted to make sure that we are getting results from the individual >> searches. Is there an issue in my search parameters which is responsible >> for the problem? >> >> Many Thanks, >> Ali >> >> On Wednesday, October 5, 2016 at 7:06:19 PM UTC-4, David Shteynberg wrote: >>> >>> Hi Ali, >>> >>> >>> Are you setting your instrument to collect only 2+ and 3+ data? Are you >>> using the tandem bundled with TPP or the GPM version of tandem? Have you >>> tried to process all your runs in one file? >>> >>> Thanks, >>> -David >>> >>> >>> On Wed, Oct 5, 2016 at 11:39 AM, Ali wrote: >>> Thank you very much! I really appreciate it! On Tuesday, October 4, 2016 at 8:03:27 PM UTC-4, David Shteynberg wrote: > > PeptideProphet is doing it's job here by telling you that there is no > distinct population of correct results in this search. I suspect your > search parameters are the problem. This is orbitrap data so the charges > should be known, but it seems Tandem only searched 2+ and 3+ for you, > this > is somewhat troubling. Tomorrow, I will check your parameters more > carefully to try to identify the actual problem with your search. > > -David > > > On Tue, Oct 4, 2016 at 2:12 PM, Ali wrote: > >> It appears that PeptideProphet fails, I am getting this message: >> >> using Accurate Mass Bins >> using PPM mass difference >> (X! Tandem) (minprob 0) >> adding Accurate Mass mixture distr >> init with X! Tandem trypsin >> MS Instrument info: Manufacturer: Thermo Scientific, Model: UNKNOWN, >> Ionization: nanoelectrospray, Analyzer: orbitrap, Detector: inductive >> detector >> >> PeptideProphet (TPP v4.8.0 PHILAE, Build 201608051257-exported >> (RedHatEnterpriseServer-x86_64)) AKeller@ISB >> read in 0 1+, 14418 2+, 11080 3+, 0 4+, 0 5+, 0 6+, and 0 7+ spectra. >> Initialising statistical models ... >> negmean = 0.0533258 >> negmean = 1 >> negmean = 0.0376944 >> negmean = -0.2 >> negmean = -0.2 >> negmean = -0.2 >> negmean = -0.2 >> Iterations: .10.20. >> WARNING: Mixture model quality test failed for charge (2+). >> WARNING: Mixture model quality test failed for charge (3+). >> >> On Monday, October 3, 2016 at 5:57:39 PM UTC-4, David Shteynberg >> wrote: >>> >>> I highly recommend you start employing decoys in your search >>> databases. I noticed you are not combining together the runs in the >>> analysis. If the data was generated and searched in the same way it >>> should >>> be analysed together for better statistical power. I suggest you >>> combine >>> the results from all your runs and filter by the spectrum names later. >>> Try >>> this: >>> >>> InteractParser ./ALL.interact.xml ./*.tandem.pep.xml -S -Etrypsin >>> PeptideProphetParser ./ALL.interact.xml ACCMASS PPM NOICAT MINPROB=0 >>> >>> >>> -David >>> >>> On Mon, Oct 3, 2016 at 2:39 PM, Ali wrote: >>> Hi David Thanks for your reply. I don't think so, it
Re: [spctools-discuss] PeptideProphet returns zero probability for all of the X!Tandem search results
I cannot tell from the search parameters if there is a problem. The only issue I saw was that you didn't enable isotopic offsets, which are sometimes helpful. If you send me a sample mzML file and possibly the search results in pep.xml along with the database I can troubleshoot further. One question, you said you are selecting 2+ 3+ and 4+, why are only 2+ and 3+ in this dataset? Does any other dataset in your analysis contain 4+? -David On Wed, Oct 5, 2016 at 6:16 PM, Ali wrote: > Hi David > > We are only collecting 2+, 3+ and 4+ data. I am working on the cluster, so > I am using the GPM version and we were unable to install the k-score plugin > therefore I am using the X! Tandem native scoring for the searches. > > If you mean combining all of the search results with xinteract and then > using PeptideProphet (as you instructed), I have not yet done so because I > wanted to make sure that we are getting results from the individual > searches. Is there an issue in my search parameters which is responsible > for the problem? > > Many Thanks, > Ali > > On Wednesday, October 5, 2016 at 7:06:19 PM UTC-4, David Shteynberg wrote: >> >> Hi Ali, >> >> >> Are you setting your instrument to collect only 2+ and 3+ data? Are you >> using the tandem bundled with TPP or the GPM version of tandem? Have you >> tried to process all your runs in one file? >> >> Thanks, >> -David >> >> >> On Wed, Oct 5, 2016 at 11:39 AM, Ali wrote: >> >>> Thank you very much! I really appreciate it! >>> >>> On Tuesday, October 4, 2016 at 8:03:27 PM UTC-4, David Shteynberg wrote: PeptideProphet is doing it's job here by telling you that there is no distinct population of correct results in this search. I suspect your search parameters are the problem. This is orbitrap data so the charges should be known, but it seems Tandem only searched 2+ and 3+ for you, this is somewhat troubling. Tomorrow, I will check your parameters more carefully to try to identify the actual problem with your search. -David On Tue, Oct 4, 2016 at 2:12 PM, Ali wrote: > It appears that PeptideProphet fails, I am getting this message: > > using Accurate Mass Bins > using PPM mass difference > (X! Tandem) (minprob 0) > adding Accurate Mass mixture distr > init with X! Tandem trypsin > MS Instrument info: Manufacturer: Thermo Scientific, Model: UNKNOWN, > Ionization: nanoelectrospray, Analyzer: orbitrap, Detector: inductive > detector > > PeptideProphet (TPP v4.8.0 PHILAE, Build 201608051257-exported > (RedHatEnterpriseServer-x86_64)) AKeller@ISB > read in 0 1+, 14418 2+, 11080 3+, 0 4+, 0 5+, 0 6+, and 0 7+ spectra. > Initialising statistical models ... > negmean = 0.0533258 > negmean = 1 > negmean = 0.0376944 > negmean = -0.2 > negmean = -0.2 > negmean = -0.2 > negmean = -0.2 > Iterations: .10.20. > WARNING: Mixture model quality test failed for charge (2+). > WARNING: Mixture model quality test failed for charge (3+). > > On Monday, October 3, 2016 at 5:57:39 PM UTC-4, David Shteynberg wrote: >> >> I highly recommend you start employing decoys in your search >> databases. I noticed you are not combining together the runs in the >> analysis. If the data was generated and searched in the same way it >> should >> be analysed together for better statistical power. I suggest you combine >> the results from all your runs and filter by the spectrum names later. >> Try >> this: >> >> InteractParser ./ALL.interact.xml ./*.tandem.pep.xml -S -Etrypsin >> PeptideProphetParser ./ALL.interact.xml ACCMASS PPM NOICAT MINPROB=0 >> >> >> -David >> >> On Mon, Oct 3, 2016 at 2:39 PM, Ali wrote: >> >>> Hi David >>> >>> Thanks for your reply. I don't think so, it is not just one set, as >>> I said almost a third of my search results are returned with zero >>> probabilities. All of the searches are done with the same setting and >>> using >>> the same database. The fact that for some of the searched files I am >>> getting zero probabilities and some of them are just fine is a bit >>> strange. >>> I don't have decoys in my data base. If it helps, I can send you one of >>> the >>> search results with or without PeptideProphet probabilities. >>> >>> Sincerely, >>> Ali >>> >>> >>> >>> On Monday, October 3, 2016 at 4:19:05 PM UTC-4, David Shteynberg >>> wrote: Is it possible there are no correct results in that set? Common pitfalls are incorrect search parameters (e.g. wrong mods enabled or disabled) and wrong database. If you have decoys in your database these can be utilized for a more accurate mixture model generation using options "DECOY= DECOYPROBS NON
Re: [spctools-discuss] PeptideProphet returns zero probability for all of the X!Tandem search results
Hi David We are only collecting 2+, 3+ and 4+ data. I am working on the cluster, so I am using the GPM version and we were unable to install the k-score plugin therefore I am using the X! Tandem native scoring for the searches. If you mean combining all of the search results with xinteract and then using PeptideProphet (as you instructed), I have not yet done so because I wanted to make sure that we are getting results from the individual searches. Is there an issue in my search parameters which is responsible for the problem? Many Thanks, Ali On Wednesday, October 5, 2016 at 7:06:19 PM UTC-4, David Shteynberg wrote: > > Hi Ali, > > > Are you setting your instrument to collect only 2+ and 3+ data? Are you > using the tandem bundled with TPP or the GPM version of tandem? Have you > tried to process all your runs in one file? > > Thanks, > -David > > > On Wed, Oct 5, 2016 at 11:39 AM, Ali > > wrote: > >> Thank you very much! I really appreciate it! >> >> On Tuesday, October 4, 2016 at 8:03:27 PM UTC-4, David Shteynberg wrote: >>> >>> PeptideProphet is doing it's job here by telling you that there is no >>> distinct population of correct results in this search. I suspect your >>> search parameters are the problem. This is orbitrap data so the charges >>> should be known, but it seems Tandem only searched 2+ and 3+ for you, this >>> is somewhat troubling. Tomorrow, I will check your parameters more >>> carefully to try to identify the actual problem with your search. >>> >>> -David >>> >>> >>> On Tue, Oct 4, 2016 at 2:12 PM, Ali wrote: >>> It appears that PeptideProphet fails, I am getting this message: using Accurate Mass Bins using PPM mass difference (X! Tandem) (minprob 0) adding Accurate Mass mixture distr init with X! Tandem trypsin MS Instrument info: Manufacturer: Thermo Scientific, Model: UNKNOWN, Ionization: nanoelectrospray, Analyzer: orbitrap, Detector: inductive detector PeptideProphet (TPP v4.8.0 PHILAE, Build 201608051257-exported (RedHatEnterpriseServer-x86_64)) AKeller@ISB read in 0 1+, 14418 2+, 11080 3+, 0 4+, 0 5+, 0 6+, and 0 7+ spectra. Initialising statistical models ... negmean = 0.0533258 negmean = 1 negmean = 0.0376944 negmean = -0.2 negmean = -0.2 negmean = -0.2 negmean = -0.2 Iterations: .10.20. WARNING: Mixture model quality test failed for charge (2+). WARNING: Mixture model quality test failed for charge (3+). On Monday, October 3, 2016 at 5:57:39 PM UTC-4, David Shteynberg wrote: > > I highly recommend you start employing decoys in your search > databases. I noticed you are not combining together the runs in the > analysis. If the data was generated and searched in the same way it > should > be analysed together for better statistical power. I suggest you combine > the results from all your runs and filter by the spectrum names later. > Try > this: > > InteractParser ./ALL.interact.xml ./*.tandem.pep.xml -S -Etrypsin > PeptideProphetParser ./ALL.interact.xml ACCMASS PPM NOICAT MINPROB=0 > > > -David > > On Mon, Oct 3, 2016 at 2:39 PM, Ali wrote: > >> Hi David >> >> Thanks for your reply. I don't think so, it is not just one set, as I >> said almost a third of my search results are returned with zero >> probabilities. All of the searches are done with the same setting and >> using >> the same database. The fact that for some of the searched files I am >> getting zero probabilities and some of them are just fine is a bit >> strange. >> I don't have decoys in my data base. If it helps, I can send you one of >> the >> search results with or without PeptideProphet probabilities. >> >> Sincerely, >> Ali >> >> >> >> On Monday, October 3, 2016 at 4:19:05 PM UTC-4, David Shteynberg >> wrote: >>> >>> Is it possible there are no correct results in that set? Common >>> pitfalls are incorrect search parameters (e.g. wrong mods enabled or >>> disabled) and wrong database. If you have decoys in your database >>> these >>> can be utilized for a more accurate mixture model generation using >>> options >>> "DECOY= DECOYPROBS NONPARAM" in additions to the >>> options you already have enabled. >>> >>> -David >>> >>> On Mon, Oct 3, 2016 at 10:39 AM, Ali wrote: >>> Hi I am using PeptideProphet on my X!Tandem search results. There are ~150 experiments and PeptideProphet works fine on most of them but for ~50 experiments, PeptideProphet returns zero probability for all of the peptides. Can some one please tell me what might be the issue? *More Info:* I am using TPP v4.8 on Linux. PeptideProp
Re: [spctools-discuss] PeptideProphet returns zero probability for all of the X!Tandem search results
Hi Ali, Are you setting your instrument to collect only 2+ and 3+ data? Are you using the tandem bundled with TPP or the GPM version of tandem? Have you tried to process all your runs in one file? Thanks, -David On Wed, Oct 5, 2016 at 11:39 AM, Ali wrote: > Thank you very much! I really appreciate it! > > On Tuesday, October 4, 2016 at 8:03:27 PM UTC-4, David Shteynberg wrote: >> >> PeptideProphet is doing it's job here by telling you that there is no >> distinct population of correct results in this search. I suspect your >> search parameters are the problem. This is orbitrap data so the charges >> should be known, but it seems Tandem only searched 2+ and 3+ for you, this >> is somewhat troubling. Tomorrow, I will check your parameters more >> carefully to try to identify the actual problem with your search. >> >> -David >> >> >> On Tue, Oct 4, 2016 at 2:12 PM, Ali wrote: >> >>> It appears that PeptideProphet fails, I am getting this message: >>> >>> using Accurate Mass Bins >>> using PPM mass difference >>> (X! Tandem) (minprob 0) >>> adding Accurate Mass mixture distr >>> init with X! Tandem trypsin >>> MS Instrument info: Manufacturer: Thermo Scientific, Model: UNKNOWN, >>> Ionization: nanoelectrospray, Analyzer: orbitrap, Detector: inductive >>> detector >>> >>> PeptideProphet (TPP v4.8.0 PHILAE, Build 201608051257-exported >>> (RedHatEnterpriseServer-x86_64)) AKeller@ISB >>> read in 0 1+, 14418 2+, 11080 3+, 0 4+, 0 5+, 0 6+, and 0 7+ spectra. >>> Initialising statistical models ... >>> negmean = 0.0533258 >>> negmean = 1 >>> negmean = 0.0376944 >>> negmean = -0.2 >>> negmean = -0.2 >>> negmean = -0.2 >>> negmean = -0.2 >>> Iterations: .10.20. >>> WARNING: Mixture model quality test failed for charge (2+). >>> WARNING: Mixture model quality test failed for charge (3+). >>> >>> On Monday, October 3, 2016 at 5:57:39 PM UTC-4, David Shteynberg wrote: I highly recommend you start employing decoys in your search databases. I noticed you are not combining together the runs in the analysis. If the data was generated and searched in the same way it should be analysed together for better statistical power. I suggest you combine the results from all your runs and filter by the spectrum names later. Try this: InteractParser ./ALL.interact.xml ./*.tandem.pep.xml -S -Etrypsin PeptideProphetParser ./ALL.interact.xml ACCMASS PPM NOICAT MINPROB=0 -David On Mon, Oct 3, 2016 at 2:39 PM, Ali wrote: > Hi David > > Thanks for your reply. I don't think so, it is not just one set, as I > said almost a third of my search results are returned with zero > probabilities. All of the searches are done with the same setting and > using > the same database. The fact that for some of the searched files I am > getting zero probabilities and some of them are just fine is a bit > strange. > I don't have decoys in my data base. If it helps, I can send you one of > the > search results with or without PeptideProphet probabilities. > > Sincerely, > Ali > > > > On Monday, October 3, 2016 at 4:19:05 PM UTC-4, David Shteynberg wrote: >> >> Is it possible there are no correct results in that set? Common >> pitfalls are incorrect search parameters (e.g. wrong mods enabled or >> disabled) and wrong database. If you have decoys in your database these >> can be utilized for a more accurate mixture model generation using >> options >> "DECOY= DECOYPROBS NONPARAM" in additions to the >> options you already have enabled. >> >> -David >> >> On Mon, Oct 3, 2016 at 10:39 AM, Ali wrote: >> >>> Hi >>> >>> I am using PeptideProphet on my X!Tandem search results. There are >>> ~150 experiments and PeptideProphet works fine on most of them but for >>> ~50 >>> experiments, PeptideProphet returns zero probability for all of the >>> peptides. Can some one please tell me what might be the issue? >>> >>> *More Info:* >>> I am using TPP v4.8 on Linux. PeptideProphet does not show an error >>> when it produces zero probability for all of the search results. >>> This is what I'm doing: >>> -search with X!Tandem >>> -Tandem2XML ./100.tandem.xml ./100.tandem.pep.xml >>> -InteractParser ./100.interact.xml ./100.tandem.pep.xml -S -Etrypsin >>> -PeptideProphetParser ./100.interact.xml ACCMASS PPM NOICAT MINPROB=0 >>> >>> >>> Thank you very much, >>> *Ali* >>> >>> -- >>> 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.goo
Re: [spctools-discuss] PeptideProphet returns zero probability for all of the X!Tandem search results
Thank you very much! I really appreciate it! On Tuesday, October 4, 2016 at 8:03:27 PM UTC-4, David Shteynberg wrote: > > PeptideProphet is doing it's job here by telling you that there is no > distinct population of correct results in this search. I suspect your > search parameters are the problem. This is orbitrap data so the charges > should be known, but it seems Tandem only searched 2+ and 3+ for you, this > is somewhat troubling. Tomorrow, I will check your parameters more > carefully to try to identify the actual problem with your search. > > -David > > On Tue, Oct 4, 2016 at 2:12 PM, Ali > > wrote: > >> It appears that PeptideProphet fails, I am getting this message: >> >> using Accurate Mass Bins >> using PPM mass difference >> (X! Tandem) (minprob 0) >> adding Accurate Mass mixture distr >> init with X! Tandem trypsin >> MS Instrument info: Manufacturer: Thermo Scientific, Model: UNKNOWN, >> Ionization: nanoelectrospray, Analyzer: orbitrap, Detector: inductive >> detector >> >> PeptideProphet (TPP v4.8.0 PHILAE, Build 201608051257-exported >> (RedHatEnterpriseServer-x86_64)) AKeller@ISB >> read in 0 1+, 14418 2+, 11080 3+, 0 4+, 0 5+, 0 6+, and 0 7+ spectra. >> Initialising statistical models ... >> negmean = 0.0533258 >> negmean = 1 >> negmean = 0.0376944 >> negmean = -0.2 >> negmean = -0.2 >> negmean = -0.2 >> negmean = -0.2 >> Iterations: .10.20. >> WARNING: Mixture model quality test failed for charge (2+). >> WARNING: Mixture model quality test failed for charge (3+). >> >> On Monday, October 3, 2016 at 5:57:39 PM UTC-4, David Shteynberg wrote: >>> >>> I highly recommend you start employing decoys in your search databases. >>> I noticed you are not combining together the runs in the analysis. If the >>> data was generated and searched in the same way it should be analysed >>> together for better statistical power. I suggest you combine the results >>> from all your runs and filter by the spectrum names later. Try this: >>> >>> InteractParser ./ALL.interact.xml ./*.tandem.pep.xml -S -Etrypsin >>> PeptideProphetParser ./ALL.interact.xml ACCMASS PPM NOICAT MINPROB=0 >>> >>> >>> -David >>> >>> On Mon, Oct 3, 2016 at 2:39 PM, Ali wrote: >>> Hi David Thanks for your reply. I don't think so, it is not just one set, as I said almost a third of my search results are returned with zero probabilities. All of the searches are done with the same setting and using the same database. The fact that for some of the searched files I am getting zero probabilities and some of them are just fine is a bit strange. I don't have decoys in my data base. If it helps, I can send you one of the search results with or without PeptideProphet probabilities. Sincerely, Ali On Monday, October 3, 2016 at 4:19:05 PM UTC-4, David Shteynberg wrote: > > Is it possible there are no correct results in that set? Common > pitfalls are incorrect search parameters (e.g. wrong mods enabled or > disabled) and wrong database. If you have decoys in your database these > can be utilized for a more accurate mixture model generation using > options > "DECOY= DECOYPROBS NONPARAM" in additions to the > options you already have enabled. > > -David > > On Mon, Oct 3, 2016 at 10:39 AM, Ali wrote: > >> Hi >> >> I am using PeptideProphet on my X!Tandem search results. There are >> ~150 experiments and PeptideProphet works fine on most of them but for >> ~50 >> experiments, PeptideProphet returns zero probability for all of the >> peptides. Can some one please tell me what might be the issue? >> >> *More Info:* >> I am using TPP v4.8 on Linux. PeptideProphet does not show an error >> when it produces zero probability for all of the search results. >> This is what I'm doing: >> -search with X!Tandem >> -Tandem2XML ./100.tandem.xml ./100.tandem.pep.xml >> -InteractParser ./100.interact.xml ./100.tandem.pep.xml -S -Etrypsin >> -PeptideProphetParser ./100.interact.xml ACCMASS PPM NOICAT MINPROB=0 >> >> >> Thank you very much, >> *Ali* >> >> -- >> 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.
Re: [spctools-discuss] PeptideProphet returns zero probability for all of the X!Tandem search results
PeptideProphet is doing it's job here by telling you that there is no distinct population of correct results in this search. I suspect your search parameters are the problem. This is orbitrap data so the charges should be known, but it seems Tandem only searched 2+ and 3+ for you, this is somewhat troubling. Tomorrow, I will check your parameters more carefully to try to identify the actual problem with your search. -David On Tue, Oct 4, 2016 at 2:12 PM, Ali wrote: > It appears that PeptideProphet fails, I am getting this message: > > using Accurate Mass Bins > using PPM mass difference > (X! Tandem) (minprob 0) > adding Accurate Mass mixture distr > init with X! Tandem trypsin > MS Instrument info: Manufacturer: Thermo Scientific, Model: UNKNOWN, > Ionization: nanoelectrospray, Analyzer: orbitrap, Detector: inductive > detector > > PeptideProphet (TPP v4.8.0 PHILAE, Build 201608051257-exported > (RedHatEnterpriseServer-x86_64)) AKeller@ISB > read in 0 1+, 14418 2+, 11080 3+, 0 4+, 0 5+, 0 6+, and 0 7+ spectra. > Initialising statistical models ... > negmean = 0.0533258 > negmean = 1 > negmean = 0.0376944 > negmean = -0.2 > negmean = -0.2 > negmean = -0.2 > negmean = -0.2 > Iterations: .10.20. > WARNING: Mixture model quality test failed for charge (2+). > WARNING: Mixture model quality test failed for charge (3+). > > On Monday, October 3, 2016 at 5:57:39 PM UTC-4, David Shteynberg wrote: >> >> I highly recommend you start employing decoys in your search databases. >> I noticed you are not combining together the runs in the analysis. If the >> data was generated and searched in the same way it should be analysed >> together for better statistical power. I suggest you combine the results >> from all your runs and filter by the spectrum names later. Try this: >> >> InteractParser ./ALL.interact.xml ./*.tandem.pep.xml -S -Etrypsin >> PeptideProphetParser ./ALL.interact.xml ACCMASS PPM NOICAT MINPROB=0 >> >> >> -David >> >> On Mon, Oct 3, 2016 at 2:39 PM, Ali wrote: >> >>> Hi David >>> >>> Thanks for your reply. I don't think so, it is not just one set, as I >>> said almost a third of my search results are returned with zero >>> probabilities. All of the searches are done with the same setting and using >>> the same database. The fact that for some of the searched files I am >>> getting zero probabilities and some of them are just fine is a bit strange. >>> I don't have decoys in my data base. If it helps, I can send you one of the >>> search results with or without PeptideProphet probabilities. >>> >>> Sincerely, >>> Ali >>> >>> >>> >>> On Monday, October 3, 2016 at 4:19:05 PM UTC-4, David Shteynberg wrote: Is it possible there are no correct results in that set? Common pitfalls are incorrect search parameters (e.g. wrong mods enabled or disabled) and wrong database. If you have decoys in your database these can be utilized for a more accurate mixture model generation using options "DECOY= DECOYPROBS NONPARAM" in additions to the options you already have enabled. -David On Mon, Oct 3, 2016 at 10:39 AM, Ali wrote: > Hi > > I am using PeptideProphet on my X!Tandem search results. There are > ~150 experiments and PeptideProphet works fine on most of them but for ~50 > experiments, PeptideProphet returns zero probability for all of the > peptides. Can some one please tell me what might be the issue? > > *More Info:* > I am using TPP v4.8 on Linux. PeptideProphet does not show an error > when it produces zero probability for all of the search results. > This is what I'm doing: > -search with X!Tandem > -Tandem2XML ./100.tandem.xml ./100.tandem.pep.xml > -InteractParser ./100.interact.xml ./100.tandem.pep.xml -S -Etrypsin > -PeptideProphetParser ./100.interact.xml ACCMASS PPM NOICAT MINPROB=0 > > > Thank you very much, > *Ali* > > -- > 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-d
Re: [spctools-discuss] PeptideProphet returns zero probability for all of the X!Tandem search results
It appears that PeptideProphet fails, I am getting this message: using Accurate Mass Bins using PPM mass difference (X! Tandem) (minprob 0) adding Accurate Mass mixture distr init with X! Tandem trypsin MS Instrument info: Manufacturer: Thermo Scientific, Model: UNKNOWN, Ionization: nanoelectrospray, Analyzer: orbitrap, Detector: inductive detector PeptideProphet (TPP v4.8.0 PHILAE, Build 201608051257-exported (RedHatEnterpriseServer-x86_64)) AKeller@ISB read in 0 1+, 14418 2+, 11080 3+, 0 4+, 0 5+, 0 6+, and 0 7+ spectra. Initialising statistical models ... negmean = 0.0533258 negmean = 1 negmean = 0.0376944 negmean = -0.2 negmean = -0.2 negmean = -0.2 negmean = -0.2 Iterations: .10.20. WARNING: Mixture model quality test failed for charge (2+). WARNING: Mixture model quality test failed for charge (3+). On Monday, October 3, 2016 at 5:57:39 PM UTC-4, David Shteynberg wrote: > > I highly recommend you start employing decoys in your search databases. I > noticed you are not combining together the runs in the analysis. If the > data was generated and searched in the same way it should be analysed > together for better statistical power. I suggest you combine the results > from all your runs and filter by the spectrum names later. Try this: > > InteractParser ./ALL.interact.xml ./*.tandem.pep.xml -S -Etrypsin > PeptideProphetParser ./ALL.interact.xml ACCMASS PPM NOICAT MINPROB=0 > > > -David > > On Mon, Oct 3, 2016 at 2:39 PM, Ali > > wrote: > >> Hi David >> >> Thanks for your reply. I don't think so, it is not just one set, as I >> said almost a third of my search results are returned with zero >> probabilities. All of the searches are done with the same setting and using >> the same database. The fact that for some of the searched files I am >> getting zero probabilities and some of them are just fine is a bit strange. >> I don't have decoys in my data base. If it helps, I can send you one of the >> search results with or without PeptideProphet probabilities. >> >> Sincerely, >> Ali >> >> >> >> On Monday, October 3, 2016 at 4:19:05 PM UTC-4, David Shteynberg wrote: >>> >>> Is it possible there are no correct results in that set? Common >>> pitfalls are incorrect search parameters (e.g. wrong mods enabled or >>> disabled) and wrong database. If you have decoys in your database these >>> can be utilized for a more accurate mixture model generation using options >>> "DECOY= DECOYPROBS NONPARAM" in additions to the >>> options you already have enabled. >>> >>> -David >>> >>> On Mon, Oct 3, 2016 at 10:39 AM, Ali wrote: >>> Hi I am using PeptideProphet on my X!Tandem search results. There are ~150 experiments and PeptideProphet works fine on most of them but for ~50 experiments, PeptideProphet returns zero probability for all of the peptides. Can some one please tell me what might be the issue? *More Info:* I am using TPP v4.8 on Linux. PeptideProphet does not show an error when it produces zero probability for all of the search results. This is what I'm doing: -search with X!Tandem -Tandem2XML ./100.tandem.xml ./100.tandem.pep.xml -InteractParser ./100.interact.xml ./100.tandem.pep.xml -S -Etrypsin -PeptideProphetParser ./100.interact.xml ACCMASS PPM NOICAT MINPROB=0 Thank you very much, *Ali* -- 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.
Re: [spctools-discuss] PeptideProphet returns zero probability for all of the X!Tandem search results
Thanks for your recommendations David. I added decoys to my data base and I am still getting 0 probabilities for all of the hits. I am attaching my X! Tandem search parameters xml, could you please kindly do me a big favor and check it to see if there is anything suspicious there which might cause the issue? I am using Trypsin enzyme and TMT 10 plex of K and TMT 10plex of N term fixed residue modification. Sincerely, *Ali* On Monday, October 3, 2016 at 5:57:39 PM UTC-4, David Shteynberg wrote: > > I highly recommend you start employing decoys in your search databases. I > noticed you are not combining together the runs in the analysis. If the > data was generated and searched in the same way it should be analysed > together for better statistical power. I suggest you combine the results > from all your runs and filter by the spectrum names later. Try this: > > InteractParser ./ALL.interact.xml ./*.tandem.pep.xml -S -Etrypsin > PeptideProphetParser ./ALL.interact.xml ACCMASS PPM NOICAT MINPROB=0 > > > -David > > On Mon, Oct 3, 2016 at 2:39 PM, Ali > > wrote: > >> Hi David >> >> Thanks for your reply. I don't think so, it is not just one set, as I >> said almost a third of my search results are returned with zero >> probabilities. All of the searches are done with the same setting and using >> the same database. The fact that for some of the searched files I am >> getting zero probabilities and some of them are just fine is a bit strange. >> I don't have decoys in my data base. If it helps, I can send you one of the >> search results with or without PeptideProphet probabilities. >> >> Sincerely, >> Ali >> >> >> >> On Monday, October 3, 2016 at 4:19:05 PM UTC-4, David Shteynberg wrote: >>> >>> Is it possible there are no correct results in that set? Common >>> pitfalls are incorrect search parameters (e.g. wrong mods enabled or >>> disabled) and wrong database. If you have decoys in your database these >>> can be utilized for a more accurate mixture model generation using options >>> "DECOY= DECOYPROBS NONPARAM" in additions to the >>> options you already have enabled. >>> >>> -David >>> >>> On Mon, Oct 3, 2016 at 10:39 AM, Ali wrote: >>> Hi I am using PeptideProphet on my X!Tandem search results. There are ~150 experiments and PeptideProphet works fine on most of them but for ~50 experiments, PeptideProphet returns zero probability for all of the peptides. Can some one please tell me what might be the issue? *More Info:* I am using TPP v4.8 on Linux. PeptideProphet does not show an error when it produces zero probability for all of the search results. This is what I'm doing: -search with X!Tandem -Tandem2XML ./100.tandem.xml ./100.tandem.pep.xml -InteractParser ./100.interact.xml ./100.tandem.pep.xml -S -Etrypsin -PeptideProphetParser ./100.interact.xml ACCMASS PPM NOICAT MINPROB=0 Thank you very much, *Ali* -- 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. input100.xml Description: XML document default_no_k.xml Description: XML document
Re: [spctools-discuss] PeptideProphet returns zero probability for all of the X!Tandem search results
I highly recommend you start employing decoys in your search databases. I noticed you are not combining together the runs in the analysis. If the data was generated and searched in the same way it should be analysed together for better statistical power. I suggest you combine the results from all your runs and filter by the spectrum names later. Try this: InteractParser ./ALL.interact.xml ./*.tandem.pep.xml -S -Etrypsin PeptideProphetParser ./ALL.interact.xml ACCMASS PPM NOICAT MINPROB=0 -David On Mon, Oct 3, 2016 at 2:39 PM, Ali wrote: > Hi David > > Thanks for your reply. I don't think so, it is not just one set, as I said > almost a third of my search results are returned with zero probabilities. > All of the searches are done with the same setting and using the same > database. The fact that for some of the searched files I am getting zero > probabilities and some of them are just fine is a bit strange. I don't have > decoys in my data base. If it helps, I can send you one of the search > results with or without PeptideProphet probabilities. > > Sincerely, > Ali > > > > On Monday, October 3, 2016 at 4:19:05 PM UTC-4, David Shteynberg wrote: >> >> Is it possible there are no correct results in that set? Common pitfalls >> are incorrect search parameters (e.g. wrong mods enabled or disabled) and >> wrong database. If you have decoys in your database these can be utilized >> for a more accurate mixture model generation using options "DECOY=> decoy prefix> DECOYPROBS NONPARAM" in additions to the options you already >> have enabled. >> >> -David >> >> On Mon, Oct 3, 2016 at 10:39 AM, Ali wrote: >> >>> Hi >>> >>> I am using PeptideProphet on my X!Tandem search results. There are ~150 >>> experiments and PeptideProphet works fine on most of them but for ~50 >>> experiments, PeptideProphet returns zero probability for all of the >>> peptides. Can some one please tell me what might be the issue? >>> >>> *More Info:* >>> I am using TPP v4.8 on Linux. PeptideProphet does not show an error when >>> it produces zero probability for all of the search results. >>> This is what I'm doing: >>> -search with X!Tandem >>> -Tandem2XML ./100.tandem.xml ./100.tandem.pep.xml >>> -InteractParser ./100.interact.xml ./100.tandem.pep.xml -S -Etrypsin >>> -PeptideProphetParser ./100.interact.xml ACCMASS PPM NOICAT MINPROB=0 >>> >>> >>> Thank you very much, >>> *Ali* >>> >>> -- >>> 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. 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.
Re: [spctools-discuss] PeptideProphet returns zero probability for all of the X!Tandem search results
Hi David Thanks for your reply. I don't think so, it is not just one set, as I said almost a third of my search results are returned with zero probabilities. All of the searches are done with the same setting and using the same database. The fact that for some of the searched files I am getting zero probabilities and some of them are just fine is a bit strange. I don't have decoys in my data base. If it helps, I can send you one of the search results with or without PeptideProphet probabilities. Sincerely, Ali On Monday, October 3, 2016 at 4:19:05 PM UTC-4, David Shteynberg wrote: > > Is it possible there are no correct results in that set? Common pitfalls > are incorrect search parameters (e.g. wrong mods enabled or disabled) and > wrong database. If you have decoys in your database these can be utilized > for a more accurate mixture model generation using options "DECOY= decoy prefix> DECOYPROBS NONPARAM" in additions to the options you already > have enabled. > > -David > > On Mon, Oct 3, 2016 at 10:39 AM, Ali > > wrote: > >> Hi >> >> I am using PeptideProphet on my X!Tandem search results. There are ~150 >> experiments and PeptideProphet works fine on most of them but for ~50 >> experiments, PeptideProphet returns zero probability for all of the >> peptides. Can some one please tell me what might be the issue? >> >> *More Info:* >> I am using TPP v4.8 on Linux. PeptideProphet does not show an error when >> it produces zero probability for all of the search results. >> This is what I'm doing: >> -search with X!Tandem >> -Tandem2XML ./100.tandem.xml ./100.tandem.pep.xml >> -InteractParser ./100.interact.xml ./100.tandem.pep.xml -S -Etrypsin >> -PeptideProphetParser ./100.interact.xml ACCMASS PPM NOICAT MINPROB=0 >> >> >> Thank you very much, >> *Ali* >> >> -- >> 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.
Re: [spctools-discuss] PeptideProphet returns zero probability for all of the X!Tandem search results
Is it possible there are no correct results in that set? Common pitfalls are incorrect search parameters (e.g. wrong mods enabled or disabled) and wrong database. If you have decoys in your database these can be utilized for a more accurate mixture model generation using options "DECOY= DECOYPROBS NONPARAM" in additions to the options you already have enabled. -David On Mon, Oct 3, 2016 at 10:39 AM, Ali wrote: > Hi > > I am using PeptideProphet on my X!Tandem search results. There are ~150 > experiments and PeptideProphet works fine on most of them but for ~50 > experiments, PeptideProphet returns zero probability for all of the > peptides. Can some one please tell me what might be the issue? > > *More Info:* > I am using TPP v4.8 on Linux. PeptideProphet does not show an error when > it produces zero probability for all of the search results. > This is what I'm doing: > -search with X!Tandem > -Tandem2XML ./100.tandem.xml ./100.tandem.pep.xml > -InteractParser ./100.interact.xml ./100.tandem.pep.xml -S -Etrypsin > -PeptideProphetParser ./100.interact.xml ACCMASS PPM NOICAT MINPROB=0 > > > Thank you very much, > *Ali* > > -- > 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. 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.
