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>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
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>>>>>>>>
>>>>>>>
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>>
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