Problem analyzing MS-GF+ data using peptideprophet tool of TPP GUI- Petunia

[Ankit Balhara]

Hi all,

I was analyzing my data using MS-GF+ and then converted its output .mzid to .pepXML using idconvert. Then I tried to analyze them using Peptideprophet of the TPP GUI 'Petunia'. I choose the Pipeline- Tandem. Then it is not showing the files, so I converted the .pepXML files to .XML format by using "save as" option in notepad. I have three files. After that I ran those files again on Peptideprophet of the TPP GUI 'Petunia'. But following error message is appearing. I also used the non-parametric model during analysis.

C:/TPP/bin/xinteract (TPP v5.1.0 Syzygy, Build 201711031215-7670 (Windows_NT-x86_64))
 PPM mode in Accurate Mass Model ...

running: "C:/TPP/bin/InteractParser "/tmp/a02972/params/MS-GF/interact.pep.xml" "PQC1_Q1.XML" "PQC1_Q2.XML" "PQC1_Q3.XML" -L"7""
 file 1: PQC1_Q1.XML
WARNING: empty raw_data in msms_run_summary tag... trying .mzML ...
WARNING: cannot open data file c:/TPP/data/params/MS-GF/PQC1_Q1.mzML in msms_run_summary tag... trying .mzXML ...
WARNING: CANNOT correct data file c:/TPP/data/params/MS-GF/PQC1_Q1.mzXML in msms_run_summary tag...
WARNING: empty raw_data in msms_run_summary tag... trying .mzML ...
WARNING: cannot open data file c:/TPP/data/params/MS-GF/PQC1_Q1.mzML in msms_run_summary tag... trying .mzXML ...
WARNING: CANNOT correct data file c:/TPP/data/params/MS-GF/PQC1_Q1.mzXML in msms_run_summary tag...
 file 2: PQC1_Q2.XML
WARNING: empty raw_data in msms_run_summary tag... trying .mzML ...
WARNING: cannot open data file c:/TPP/data/params/MS-GF/PQC1_Q2.mzML in msms_run_summary tag... trying .mzXML ...
WARNING: CANNOT correct data file c:/TPP/data/params/MS-GF/PQC1_Q2.mzXML in msms_run_summary tag...
WARNING: empty raw_data in msms_run_summary tag... trying .mzML ...
WARNING: cannot open data file c:/TPP/data/params/MS-GF/PQC1_Q2.mzML in msms_run_summary tag... trying .mzXML ...
WARNING: CANNOT correct data file c:/TPP/data/params/MS-GF/PQC1_Q2.mzXML in msms_run_summary tag...
 file 3: PQC1_Q3.XML
WARNING: empty raw_data in msms_run_summary tag... trying .mzML ...
WARNING: cannot open data file c:/TPP/data/params/MS-GF/PQC1_Q3.mzML in msms_run_summary tag... trying .mzXML ...
WARNING: CANNOT correct data file c:/TPP/data/params/MS-GF/PQC1_Q3.mzXML in msms_run_summary tag...
WARNING: empty raw_data in msms_run_summary tag... trying .mzML ...
WARNING: cannot open data file c:/TPP/data/params/MS-GF/PQC1_Q3.mzML in msms_run_summary tag... trying .mzXML ...
WARNING: CANNOT correct data file c:/TPP/data/params/MS-GF/PQC1_Q3.mzXML in msms_run_summary tag...
 processed altogether 13489 results
INFO: Results written to file: /tmp/a02972/params/MS-GF/interact.pep.xml
command completed in 6 sec 

running: "C:/TPP/bin/DatabaseParser "/tmp/a02972/params/MS-GF/interact.pep.xml""
command completed in 0 sec 

running: "C:/TPP/bin/RefreshParser "/tmp/a02972/params/MS-GF/interact.pep.xml" "C:\MS-GF\Human.fasta""

  - Searching the tree...
  - Linking duplicate entries...
  - Printing results...

  - Building Commentz-Walter keyword tree...command completed in 4 sec 

running: "C:/TPP/bin/PeptideProphetParser "/tmp/a02972/params/MS-GF/interact.pep.xml" MINPROB=0.05 PPM NONPARAM"
using PPM mass difference
WARNING: Cannot non-parametric distributions without decoys!
 (MS-GF+)
WARNING: Support of MSGF+ may not be full.  There exist known issues with the way MSGF+ encodes certain modifications in pep.xml that may not be correct. Also, high-scoring DECOY have been observed in MSGF+ analysis.  The user is encouraged to be vigilant in comparing model estimated error-rates to the DECOY-estimated error-rates to make sure the two agree and set CLEVEL parameter accordingly: see http://tools.proteomecenter.org/wiki/index.php?title=TPP:Frequently_Asked_Questions#What_is_CLEVEL_and_when_do_I_use_it.3F
WARNING: MSGFPL only support semi-parametric PeptideProphet modelling, which relies on a DECOY search.
WARNING: MSGFPL only support semi-parametric PeptideProphet modelling, which relies on a DECOY search.
WARNING: MSGFPL only support semi-parametric PeptideProphet modelling, which relies on a DECOY search.
WARNING: MSGFPL only support semi-parametric PeptideProphet modelling, which relies on a DECOY search.
WARNING: MSGFPL only support semi-parametric PeptideProphet modelling, which relies on a DECOY search.
WARNING: MSGFPL only support semi-parametric PeptideProphet modelling, which relies on a DECOY search.
WARNING: MSGFPL only support semi-parametric PeptideProphet modelling, which relies on a DECOY search.
init with MS-GF+ trypsin 
MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN

INFO: Processing standard MixtureModel ... 
 PeptideProphet  (TPP v5.1.0 Syzygy, Build 201711031215-7670 (Windows_NT-x86_64)) AKeller@ISB
 read in 0 1+, 6282 2+, 5137 3+, 1488 4+, 0 5+, 0 6+, and 0 7+ spectra.
Initialising statistical models ...
Iterations: .........10.........20

command "C:/TPP/bin/PeptideProphetParser "/tmp/a02972/params/MS-GF/interact.pep.xml" MINPROB=0.05 PPM NONPARAM" failed: Unknown error

command "C:/TPP/bin/PeptideProphetParser "/tmp/a02972/params/MS-GF/interact.pep.xml" MINPROB=0.05 PPM NONPARAM" exited with non-zero exit code: -1073741819
QUIT - the job is incomplete

Could anybody please help me out to fix this problem.

Thanks.

[Alejandro]

Hi Ankit,

For me it works as follows:

1. Convert with idconvert: idconvert file.mzid --pepXML

2. Then change the extension of the files from *.pepXML to *.pep.xml then you will se them in Petunia.

3. The use Update Paths in Petunia to update the paths of the Raw files and database. (That's one of the errors as it cannot find were the RAW files are located.

Sometimes the pepxml generated has a different path structure and this leads to errors when running the TPP tools.

Best,

Alejandro

[Ankit Balhara]

Hi Alejandro,

Thanks a lot for your help, I tried this approach, and it is working.

Regards

Ankit

Sender notified by Mailtrack 06/02/19, 2:26:55 PM

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