xinteract (TPP v5.2.0) not detecting any spectra from comet output

[dfermin]

Hello 

I performed a search on 4 mzML files against a human proteome file with decoys appended. The decoy prefix I'm using is 'rev_'

I ran comet version 2020.01 rev 3 on the mzML file and got out the comet-generated pep.xml files. 

When I run xinteract on these files  PeptideProphet seems unable to find any spectra.

I've looked at the pep.xml files comet generated and it has all the usual features. The files contain the top 5 hits for each spectra. 

Any suggestions what might be wrong?

Thanks in advance for any and all help.

I'm running TPP v5.2.0 on a Centos 7  box in case it helps

Here is the stdout on the terminal:

#==================================================================

[dfermin tmp]$ xinteract -Opwd -drev *.pep.xml

xinteract (TPP v5.2.0 Flammagenitus, Build 201904020842-exported (Linux-x86_64))

running: "/usr/local/apps/tpp/bin/InteractParser 'interact.pep.xml' '01347_H01_P013678_S00_N08_R2.pep.xml' '01347_H02_P013678_S00_N16_R2.pep.xml' '01347_H03_P013678_S00_N24_R2.pep.xml' '01347_H04_P013678_S00_N32_R2.pep.xml' -L'7'"

 file 1: 01347_H01_P013678_S00_N08_R2.pep.xml

 file 2: 01347_H02_P013678_S00_N16_R2.pep.xml

 file 3: 01347_H03_P013678_S00_N24_R2.pep.xml

 file 4: 01347_H04_P013678_S00_N32_R2.pep.xml

 processed altogether 203112 results

INFO: Results written to file: /nfs/md0/testRun2021/interact.pep.xml

command completed in 104 sec

running: "/usr/local/apps/tpp/bin/DatabaseParser 'interact.pep.xml'"

command completed in 1 sec

running: "/usr/local/apps/tpp/bin/RefreshParser 'interact.pep.xml' '/nfs/md0/tpp.data/human_uniprot_withIsoforms.2021-04-14.plusREV.fa'"

  - Building Commentz-Walter keyword tree...

  - Searching the tree...

  - Linking duplicate entries...

  - Printing results...

command completed in 62 sec

running: "/usr/local/apps/tpp/bin/PeptideProphetParser 'interact.pep.xml' INSTRWARN DECOYPROBS DECOY=rev"

Using no error on different instrument types.

Using Decoy Label "rev".

Decoy Probabilities will be reported.

 (Comet)

init with Comet trypsin

MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN

INFO: Processing standard MixtureModel ...

 PeptideProphet  (TPP v5.2.0 Flammagenitus, Build 201904020842-exported (Linux-x86_64)) AKeller@ISB

 read in 0 1+, 0 2+, 0 3+, 0 4+, 0 5+, 0 6+, and 0 7+ spectra.

 read in no data

command "/usr/local/apps/tpp/bin/PeptideProphetParser 'interact.pep.xml' INSTRWARN DECOYPROBS DECOY=rev" exited with non-zero exit code: 256

QUIT - the job is incomplete

[David Shteynberg]

Hi Damian,

Unfortunately, TPP 5.2.0 is not forward compatible to comet 2020.  We are working on the 6.0.0 release and have a couple of release candidates available.   I will post another rc tomorrow. 

Cheers,

David 

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[Jimmy Eng]

Damian,

As David noted, in Comet 2020 I unfortunately got rid of a search score that causes the behavior you're seeing.  And yes, if I could go back in time, I would not have made that change again because of this noted issue.  As a quick intermediate fix until you've updated to the TPP 6 release, run this command on your pep.xml files which should then allow them to be processed through the older TPP versions.

perl -i -pe 's/<search_score name="deltacn"/<search_score name="deltacnstar" value="0.0"\/>\n <search_score name="deltacn"/g;' yourfile.pep.xml

[dfermin]

Thanks for the quick reply!

 Jimmy's command worked like a charm.

Thanks!