peptide prophet "read in no data"

[Delphine]

Hello,
I get this error when I'm using peptideprophet and I would like to understand the meaning of the "read in no data", which seems to be the beginning of the problem.
Could someone help me?
Thanks

Delphine

PS: TPP output: 


SUCCESS: CORRECTED data file C:/Inetpub/wwwroot/ISB/data/test_mslite/TCGA_114C_59-2372-01A-01_24-1548-01A-01_29-1762-01A-01_W_JHUZ_20130903_F1.mzXML in msms_run_summary tag ...
 processed altogether 5 results
INFO: Results written to file: c:/Inetpub/wwwroot/ISB/data/test_mslite/interact.pep.xml
command completed in 1.403e+009 sec 

running: "C:/Inetpub/tpp-bin/DatabaseParser "interact.pep.xml""
command completed in 1.403e+009 sec 

running: "C:/Inetpub/tpp-bin/RefreshParser "interact.pep.xml" "C:/Inetpub/wwwroot/ISB/data/test_mslite/human.protein.faa""
  - Searching the tree...
  - Linking duplicate entries...  - Printing results...

  - Building Commentz-Walter keyword tree...command completed in 1.403e+009 sec 

running: "C:/Inetpub/tpp-bin/PeptideProphetParser "interact.pep.xml" MINPROB=0.0"
 (SEQUEST) (minprob 0)
init with SEQUEST trypsin 
MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN

 PeptideProphet  (TPP v4.7 POLAR VORTEX rev 0, Build 201402281256 (MinGW)) AKeller@ISB
 read in 0 1+, 0 2+, 0 3+, 0 4+, 0 5+, 0 6+, and 0 7+ spectra.
 read in no data

[David Shteynberg]

Hi Delphine,

Perhaps all of the 5 peptides in the file are not of sufficient length
and get set to is_rejected="1" in the pepXML file after
InteractParser, so PeptideProphet cannot use them. Also 5 peptides
are much to few to get a meaningful PeptideProphet result.

-David

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[David Shteynberg]

Just to clarify, by "peptides" in the previous message I really meant
PSMs (peptide spectrum matches) listed as <spectrum_query.... elements
in the pepXML file.

-David

[delphine wood]

Hi David,

My aim was not to get a meaningful result but to see if peptideprophet could work with the pepxml I'm trying.

I used the M2Lite software to transform msf files to pepxml files. The problem is that this option is not yet completely finished and thus I'm looking for the changes requiered so that the pepxml works with peptideprophet. In the example I pasted in the post there were only five peptides because I wanted to see if adding values for "deltacn", "sscan","spscore" and "sprank" would help; with 10 peptides it still doesn't work...

I checked the is_rejected="1" in the file created during the begining of peptideprophet and not all the peptides were rejected...

Without the sequest variables and with many peptides I still get the same problem of "read in no data"... Could you tell me  what can cause this problem? I don't really know where to look now...

Thanks

Delphine

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[Eric Deutsch]

There are many things that could be wrong. It would probably be most efficient if you would make available to us some of these files, perhaps the originals and ones that you have attempted to fix. We could probably come up with an example of a file that can be processing by PeptideProphet and then you could ask the M2Lite developers to fix the exported pepXML to be complete.

 

Regards,

Eric

[David Shteynberg]

Hello Delphine,

I believe your pepXML file specifies search_engine="SEQUEST" and only
lists the xcorr aunder the search_score tag . PeptideProphet will
expect each spectrum_query/search_hit to have the following scores:

<search_score name="xcorr" value="2.696"/>
<search_score name="deltacn" value="0.408"/>
<search_score name="deltacnstar" value="0"/>
<search_score name="spscore" value="400.7"/>
<search_score name="sprank" value="2"/>


PeptideProphet only utilizes search_hits of hit_rank="1"

-David