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]> 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/0B5i2NDdAgrJ3bDY4ZFR0M >>>>>>> 2VOUlU/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/PeptideProphetP >>>>>>>>>> arser.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.co >>>>>>>>>>> m/file/d/0B5i2NDdAgrJ3Y2diWDAzVHBQSm8/view?usp=sharing) >>>>>>>>>>> >>>>>>>>>>> <spectrum_query spectrum="C:\Users\JONGHUN\Des >>>>>>>>>>> ktop\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/grou >>>>>>>>>>> p/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]. > 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. 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