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] <javascript:> > > 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] <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.
