Oops, I've been using an older version. I will try the latest version. Thanks for your quick reply!
- Jonghun On Wednesday, December 13, 2017 at 3:30:17 AM UTC+9, David Shteynberg wrote: > > Hi Jonghun, > > The link to dropbox was never meant to be permanent. The changes in that > binary should have been integrated into the release version of > PeptideProphet, installed as part of TPP 5.1.0 Which version of the TPP > are you running? > > Thanks, > -David > > On Mon, Dec 11, 2017 at 8:16 PM, Jonghun Park <[email protected] > <javascript:>> wrote: > >> Hi, >> >> I've just found this post while I'm struggling with the same problem. >> However, the link above ( >> https://dl.dropboxusercontent.com/u/21286225/PeptideProphetParser.exe) >> was broken. >> Could I get a new link or website to get the file for MSGF+? >> >> Thanks, >> >> Jonghun Park >> >> On Wednesday, July 6, 2016 at 3:25:27 PM UTC+9, David Shteynberg wrote: >>> >>> Hi Honglan, >>> >>> Thanks for using the tools! >>> >>> In my experience, searches against databases that do not contain decoys >>> are fraught with false positives and are not recommended. Unsupervised >>> support exists for legacy support of certain search engines, however, even >>> in those cases you are less likely to arrive at false results if you >>> include decoys in the database. >>> >>> >>> Cheers, >>> -David >>> >>> On Tue, Jul 5, 2016 at 9:23 PM, Honglan Li <[email protected]> wrote: >>> >>>> Hi David, >>>> >>>> Thank you so much again for sending me the new version of >>>> PeptideProphet. >>>> It runs well with MSGF+. >>>> >>>> Now, we are comparing other modes of PeptideProphet including >>>> unsupervised. Thus, I am just wondering if I can use PeptideProphet in >>>> unsupervised mode with MSGF+. >>>> >>>> All the best, >>>> Honglan >>>> >>>> >>>> >>>> 2016년 5월 2일 월요일 오후 1시 54분 39초 UTC+9, Honglan Li 님의 말: >>>> >>>>> Thanks a lot. >>>>> >>>>> These days, I tested all of my sample data as you told me. >>>>> >>>>> ALL of them worked well. >>>>> >>>>> Thank you for helping me. >>>>> >>>>> >>>>> ---One more thing: >>>>> >>>>> I use idconvert to change mzid file to pepXML fomat. >>>>> >>>>> The scan information in changed pepXML is not equal to real scan >>>>> information. >>>>> >>>>> I checked the file, and found that the scan information in changed >>>>> PepXML file is same as the 'index" of MGF file. >>>>> >>>>> Am I right? >>>>> >>>>> I just want to confirm it. >>>>> >>>>> >>>>> Honglan Li. >>>>> >>>>> >>>>> >>>>> 2016년 4월 19일 화요일 오전 2시 44분 21초 UTC+9, David Shteynberg 님의 말: >>>>>> >>>>>> Hello Honglan, >>>>>> >>>>>> >>>>>> It appears that the paths to your data contain some restricted >>>>>> characters. The only allowed characters when naming paths that are >>>>>> compatible with the TPP are alpha-numeric and '_' (underscore) ('.' and >>>>>> whitespace are disallowed.) That doesn't mean that it won't work >>>>>> sometimes >>>>>> when the paths contain restricted character, but it can be hit or miss. >>>>>> >>>>>> Please rename the directories and redo analysis. >>>>>> >>>>>> -David >>>>>> >>>>>> >>>>>> >>>>>> On Wed, Apr 13, 2016 at 7:40 AM, David Shteynberg < >>>>>> [email protected]> wrote: >>>>>> >>>>>>> Hi Honglan, >>>>>>> >>>>>>> I am on vacation this week. I did fix another processing issue with >>>>>>> MSGF+ earlier, but I was still testing. I will get back to you once >>>>>>> I'm >>>>>>> back next week. >>>>>>> >>>>>>> David >>>>>>> On Apr 13, 2016 12:14 AM, "Honglan Li" <[email protected]> wrote: >>>>>>> >>>>>>>> Hi David >>>>>>>> >>>>>>>> It's me again. >>>>>>>> >>>>>>>> Thanks for giving me new PeptideProphet file to run MS_GF+ results. >>>>>>>> >>>>>>>> But it still has problem to execute new test file. >>>>>>>> >>>>>>>> Would you please tell me the reason? >>>>>>>> >>>>>>>> >>>>>>>> Thanks a lot. >>>>>>>> >>>>>>>> Honglan Li >>>>>>>> >>>>>>>> >>>>>>>> XML file: >>>>>>>> https://drive.google.com/file/d/0B5i2NDdAgrJ3bDY4ZFR0M2VOUlU/view?usp=sharing >>>>>>>> >>>>>>>> Recieved msg: >>>>>>>> >>>>>>>> ---- >>>>>>>> KDModel.cpp, Line 144 >>>>>>>> Expression: idx < posprobs_ -> size() >>>>>>>> >>>>>>>> This application has requested the Runtime to terminate it in an >>>>>>>> unusual way. >>>>>>>> Please contact the application's support team for more information >>>>>>>> ---- >>>>>>>> >>>>>>>> Thanks a lot. >>>>>>>> >>>>>>>> Honglan Li >>>>>>>> >>>>>>>> >>>>>>>> 2016년 3월 30일 수요일 오후 8시 30분 5초 UTC+9, Honglan Li 님의 말: >>>>>>>>> >>>>>>>>> >>>>>>>>> Hi David. >>>>>>>>> >>>>>>>>> It's me again. >>>>>>>>> >>>>>>>>> Last time, you gave me the s/w and cmd. >>>>>>>>> >>>>>>>>> It's works well when I use the sample I gave you, and some other >>>>>>>>> XML files. >>>>>>>>> >>>>>>>>> But for some XML files, it still do not work well. >>>>>>>>> >>>>>>>>> XML file: >>>>>>>>> https://drive.google.com/file/d/0B5i2NDdAgrJ3bDY4ZFR0M2VOUlU/view?usp=sharing >>>>>>>>> >>>>>>>>> >>>>>>>>> When I executed this test sample (test2.pep.xml.xml) with the cmd >>>>>>>>> you told me >>>>>>>>> >>>>>>>>> "PeptideProphetParser.exe test2.pep.xml.xml >>>>>>>>> NONPARAM DECOY=XXX DECOYPROBS MINPROB=0 CLEVEL=2 ACCMASS PPM" >>>>>>>>> >>>>>>>>> I received msg as follows: (detail: I added captured error msg >>>>>>>>> file) >>>>>>>>> >>>>>>>>> ---- >>>>>>>>> KDModel.cpp, Line 144 >>>>>>>>> Expression: idx < posprobs_ -> size() >>>>>>>>> >>>>>>>>> This application has requested the Runtime to terminate it in an >>>>>>>>> unusual way. >>>>>>>>> Please contact the application's support team for more information >>>>>>>>> ---- >>>>>>>>> >>>>>>>>> Would you please tell me what happened to this XML file? >>>>>>>>> >>>>>>>>> Thanks a lot. >>>>>>>>> >>>>>>>>> Honglan Li >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> 2016년 3월 28일 월요일 오전 8시 52분 13초 UTC+9, Honglan Li 님의 말: >>>>>>>>>> >>>>>>>>>> Thank you very much for your help, David. >>>>>>>>>> >>>>>>>>>> It works well now. >>>>>>>>>> >>>>>>>>>> Best wishes, >>>>>>>>>> Honglan Li >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> 2016년 3월 26일 토요일 오전 2시 33분 59초 UTC+9, David Shteynberg 님의 말: >>>>>>>>>>> >>>>>>>>>>> Hello Honglan, >>>>>>>>>>> >>>>>>>>>>> I was unable to replicate the error on my system, however, I >>>>>>>>>>> have tested that this command works on a more recently compiled >>>>>>>>>>> version of >>>>>>>>>>> PeptideProphet. You can download the binary here >>>>>>>>>>> https://dl.dropboxusercontent.com/u/21286225/PeptideProphetParser.exe >>>>>>>>>>> >>>>>>>>>>> and run as follows >>>>>>>>>>> >>>>>>>>>>> PeptideProphetParser.exe test.pep.xml NONPARAM DECOY=XXX >>>>>>>>>>> DECOYPROBS MINPROB=0 CLEVEL=2 ACCMASS PPM >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> I had to set a fairly high CLEVEL value on this data since MSGF+ >>>>>>>>>>> suffers from scoring highly of some decoys and is not always >>>>>>>>>>> accurate at >>>>>>>>>>> the critical 1% error. The WARNING message in the new code has >>>>>>>>>>> been >>>>>>>>>>> updated to reflect this problem. >>>>>>>>>>> >>>>>>>>>>> Cheers, >>>>>>>>>>> -David >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> On Thu, Mar 24, 2016 at 8:21 PM, Honglan Li <[email protected]> >>>>>>>>>>> wrote: >>>>>>>>>>> >>>>>>>>>>>> Thanks for your quick reply. >>>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> I tried the command you told me, but it stll didn't work >>>>>>>>>>>> well. >>>>>>>>>>>> >>>>>>>>>>>> The warning msg is "*The discriminant function for MSGFPL >>>>>>>>>>>> is not yet complete" * >>>>>>>>>>>> >>>>>>>>>>>> How to fix it ? >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> *cmd*: >>>>>>>>>>>> >>>>>>>>>>>> xinteract -OPd -p0 -dXXX_ *.xml >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> *Error msg I received* >>>>>>>>>>>> >>>>>>>>>>>> ---- >>>>>>>>>>>> running: "/usr/local/tpp/bin/DatabaseParser 'interact.pep.xml'" >>>>>>>>>>>> command completed in 0 sec >>>>>>>>>>>> >>>>>>>>>>>> running: "/usr/local/tpp/bin/RefreshParser 'interact.pep.xml' >>>>>>>>>>>> 'C:\Users\JONGHUN\Desktop\MSGFPlus\C-25fmol\C-25fmol-R1\1. >>>>>>>>>>>> CYH\uniprot_C+H+Y+48.revCat.fasta'" >>>>>>>>>>>> - Building Commentz-Walter keyword tree... - Searching the >>>>>>>>>>>> tree...opening >>>>>>>>>>>> "C:\Users\JONGHUN\Desktop\MSGFPlus\C-25fmol\C-25fmol-R1\1. >>>>>>>>>>>> CYH\uniprot_C+H+Y+48.revCat.fasta" as >>>>>>>>>>>> "/home/mllab/hllee/uniprot_C+H+Y+48.revCat.fasta" >>>>>>>>>>>> >>>>>>>>>>>> - Linking duplicate entries... - Printing results... >>>>>>>>>>>> >>>>>>>>>>>> command completed in 11 sec >>>>>>>>>>>> >>>>>>>>>>>> running: "/usr/local/tpp/bin/PeptideProphetParser >>>>>>>>>>>> 'interact.pep.xml' NONPARAM DECOYPROBS MINPROB=0 DECOY=XXX_" >>>>>>>>>>>> Using Decoy Label "XXX_". >>>>>>>>>>>> Decoy Probabilities will be reported. >>>>>>>>>>>> Using non-parametric distributions >>>>>>>>>>>> (MS-GF+) (minprob 0) >>>>>>>>>>>> WARNING!! *The discriminant function for MSGFPL is not yet >>>>>>>>>>>> complete.* It is presented here to help facilitate trial and >>>>>>>>>>>> discussion. Reliance on this code for publishable scientific >>>>>>>>>>>> results is >>>>>>>>>>>> not recommended. >>>>>>>>>>>> init with MS-GF+ trypsin >>>>>>>>>>>> Segmentation fault (core dumped) >>>>>>>>>>>> >>>>>>>>>>>> command "/usr/local/tpp/bin/PeptideProphetParser >>>>>>>>>>>> 'interact.pep.xml' NONPARAM DECOYPROBS MINPROB=0 DECOY=XXX_" >>>>>>>>>>>> exited with >>>>>>>>>>>> non-zero exit code: 35584 >>>>>>>>>>>> QUIT - the job is incomplete >>>>>>>>>>>> >>>>>>>>>>>> ----- >>>>>>>>>>>> >>>>>>>>>>>> *XML format per PSM: (file: * >>>>>>>>>>>> https://drive.google.com/file/d/0B5i2NDdAgrJ3Y2diWDAzVHBQSm8/view?usp=sharing >>>>>>>>>>>> ) >>>>>>>>>>>> >>>>>>>>>>>> <spectrum_query >>>>>>>>>>>> spectrum="C:\Users\JONGHUN\Desktop\MSGFPlus\C-25fmol\C-25fmol-R1\1. >>>>>>>>>>>> >>>>>>>>>>>> CYH\C-25fmol-R1_QEx2_000090.51174.51174.4" >>>>>>>>>>>> spectrumNativeID="index=51174" >>>>>>>>>>>> start_scan="51174" end_scan="51174" >>>>>>>>>>>> precursor_neutral_mass="3972.990669523105" assumed_charge="4" >>>>>>>>>>>> index="1"> >>>>>>>>>>>> <search_result> >>>>>>>>>>>> <search_hit hit_rank="1" >>>>>>>>>>>> peptide="VGNVGEDDAIPEVSHAGDVSTTLQVVNELLKDETVAPR" >>>>>>>>>>>> peptide_prev_aa="R" >>>>>>>>>>>> peptide_next_aa="F" protein="sp|P16521|EF3A_YEAST" >>>>>>>>>>>> num_tot_proteins="1" >>>>>>>>>>>> calc_neutral_pep_mass="3972.99140194498" massdiff="7.32421875e-04" >>>>>>>>>>>> protein_descr="sp|P16521|EF3A_YEAST Elongation factor 3A >>>>>>>>>>>> OS=Saccharomyces >>>>>>>>>>>> cerevisiae (strain ATCC 204508 / S288c) GN=YEF3 PE=1 SV=4" >>>>>>>>>>>> num_tol_term="2" >>>>>>>>>>>> num_missed_cleavages="1"> >>>>>>>>>>>> <search_score name="raw" value="269"/> >>>>>>>>>>>> <search_score name="denovo" value="289"/> >>>>>>>>>>>> <search_score name="SpecEValue" >>>>>>>>>>>> value="2.8337685502588284E-39"/> >>>>>>>>>>>> <search_score name="EValue" >>>>>>>>>>>> value="1.2856572993111488E-31"/> >>>>>>>>>>>> <search_score name="IsotopeError" value="0"/> >>>>>>>>>>>> </search_hit> >>>>>>>>>>>> </search_result> >>>>>>>>>>>> </spectrum_query> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> -- >>>>>>>>>>>> You received this message because you are subscribed to the >>>>>>>>>>>> Google Groups "spctools-discuss" group. >>>>>>>>>>>> To unsubscribe from this group and stop receiving emails from >>>>>>>>>>>> it, send an email to [email protected]. >>>>>>>>>>>> To post to this group, send email to >>>>>>>>>>>> [email protected]. >>>>>>>>>>>> Visit this group at >>>>>>>>>>>> https://groups.google.com/group/spctools-discuss. >>>>>>>>>>>> For more options, visit https://groups.google.com/d/optout. >>>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> -- >>>>>>>> You received this message because you are subscribed to the Google >>>>>>>> Groups "spctools-discuss" group. >>>>>>>> To unsubscribe from this group and stop receiving emails from it, >>>>>>>> send an email to [email protected]. >>>>>>>> To post to this group, send email to [email protected]. >>>>>>>> Visit this group at >>>>>>>> https://groups.google.com/group/spctools-discuss. >>>>>>>> For more options, visit https://groups.google.com/d/optout. >>>>>>>> >>>>>>> >>>>>> -- >>>> You received this message because you are subscribed to the Google >>>> Groups "spctools-discuss" group. >>>> To unsubscribe from this group and stop receiving emails from it, send >>>> an email to [email protected]. >>>> To post to this group, send email to [email protected]. >>>> Visit this group at https://groups.google.com/group/spctools-discuss. >>>> For more options, visit https://groups.google.com/d/optout. >>>> >>> >>> -- >> You received this message because you are subscribed to the Google Groups >> "spctools-discuss" group. >> To unsubscribe from this group and stop receiving emails from it, send an >> email to [email protected] <javascript:>. >> To post to this group, send email to [email protected] >> <javascript:>. >> Visit this group at https://groups.google.com/group/spctools-discuss. >> For more options, visit https://groups.google.com/d/optout. >> > > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
