Hi Toan,

We invoked ProteinProphet indirectly through xinteract. xinteract is building up the ProteinProphet command-line, and adding that NOPLOT argument.

Is there any more detail about the error later in the log file? The line you included is just the command-line we're running.

I believe xinteract is generating the NOPLOT argument in response to the -Opt option we pass to it. Does xinteract still advertise this as a supported command-line option? You can check by manually running xinteract with no arguments on the command-line:

...
 PeptideProphet options [following the 'O']:
...
                 p [run ProteinProphet afterwards]
                 t [do not create png data plot]
...


Thanks,
Josh

Hi Josh,

  xinteract still have the "t" option. However; ProteinProphet int TPP 5.0 no longer have "NOPLOT"
  See comparison of options for ProteinProphet in tpp 4.3 and 5.0

Thanks
Toan.

$ /usr/local/tpp/bin/ProteinProphet.tpp.5.0.0
ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v5.0.0 Typhoon, Build 201710251406-7644 (Linux-x86_64))
Usage: ProteinProphet <interact_pepxml_file1> [<interact_pepxml_file2>[....]] <output_protxml_file> [OPTIONS]
Options:
        IPROPHET Input is from iProphet
        XPRESS Compute XPRESS ratios for protein entries
                        (XPRESS must have been run previously on all input datasets)
        ASAP_PROPHET Compute ASAP ratios for protein entries
                        (ASAPRatio must have been run previously on all input datasets)
        LIBRA<file> Compute Libra ratios for protein entries, using condition parameters in <file>
                        (Libra must have been run previously on all input datasets)
        EXCLUDE_ZEROS Exclude zero prob entries
        NOPROTLEN Do not report protein length
        PROTMW Get protein mol weights
        ICAT Highlight peptide cysteines
        GLYC Highlight peptide N-glycosylation motif
        PLOTPNG Generate plot png file
        FPKM Model protein FPKM values
        NONSP Do not use NSP model
        MININDEP Minimum percentage of independent peptides required for a protein (default:0)
        MINPROBxx PeptideProphet probabilty threshold (default=0.05)
        ACCURACY Equivalent to MINPROB0
        NORMPROTLEN Normalize NSP using Protein Length
        NOGROUPWTS Check peptide's Protein weight against the threshold (default: check peptide's Protein Group weight against threshold)
        INSTANCES Use Expected Number of Ion Instances to adjust the peptide probabilities prior to NSP adjustment
        DELUDE Do NOT use peptide degeneracy information when assessing proteins
        NOOCCAM Non-conservative maximum protein list
        SOFTOCCAM Peptide weights are apportioned equally among proteins within each Protein Group (less conservative protein count estimate)
        CONFEM Use the EM to compute probability given the confidence
          LOGPROBS Use the log of the probabilities in the Confidence calculations
          ALLPEPS Consider all possible peptides in the database in the confidence model
          MUFACTOR Fudge factor to scale MU calculation (default 1)
        UNMAPPED Report results for UNMAPPED proteins
        EXCELPEPS Write output tab delim xls file including all peptides
        EXCELxx Write output tab delim xls file including all protein (group)s
                        with minimum probability xx, where xx is a number between 0 and 1

$ /usr/local/tpp/bin/ProteinProphet
ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v4.3 JETSTREAM rev 1, Build 201011301302 (linux))
usage: ProteinProphet <interact_pepxml_file1> [<interact_pepxml_file2>[....]] <output_protxml_file> (ICAT) (GLYC) (XPRESS) (ASAP_PROPHET) (ACCURACY) (ASAP) (PROTLEN) (NORMPROTLEN) (GROUPWTS) (INSTANCES) (REFRESH) (DELUDE) (NOOCCAM) (NOPLOT) (PROTMW)
                NOPLOT: do not generate plot png file
                NOOCCAM: non-conservative maximum protein list
                ICAT: highlight peptide cysteines
                GLYC: highlight peptide N-glycosylation motif
                MINPROB: peptideProphet probabilty threshold (default=0.05)
                MININDEP: minimum percentage of independent peptides required for a protein (default=0)
                GROUPWTS: check peptide's total weight in the Protein Group against the threshold (default: check peptide's actual weight against threshold)
                ACCURACY: equivalent to MINPROB0
                ASAP: compute ASAP ratios for protein entries
                        (ASAP must have been run previously on interact dataset)
                REFRESH: import manual changes to AAP ratios
                        (after initially using ASAP option)
                NORMPROTLEN: Normalize NSP using Protein Length
                LOGPROBS: Use the log of the probabilities in the Confidence calculations
                CONFEM: Use the EM to compute probability given the confidence
                ALLPEPS: Consider all possible peptides in the database in the confidence model
                MUFACTOR: Fudge factor to scale MU calculation (default 1)
                UNMAPPED: Report results for UNMAPPED proteins
                PROTLEN: Report Protein Length
                INSTANCES: Use Expected Number of Ion Instances to adjust the peptide probabilities prior to NSP adjustment
                PROTMW: Get protein mol weights
                IPROPHET: input is from iProphet
                ASAP_PROPHET: *New and Improved* compute ASAP ratios for protein entries
                        (ASAP must have been run previously on all input interact datasets with mz/XML raw data format)
                DELUDE: do NOT use peptide degeneracy information when assessing proteins
                EXCELPEPS: write output tab delim xls file including all peptides
                EXCELxx: write output tab delim xls file including all protein (group)s
                                with minimum probability xx, where xx is a number between 0 and 1

/usr/local/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201710251406-7644 (Linux-x86_64))
PeptideProphet options [following the '-O']:
                 i [use icat information in PeptideProphet]
                 f [do not use icat information in PeptideProphet]
                 g [use N-glyc motif information in PeptideProphet]
                 H [use Phospho information in PeptideProphet]
                 m [maldi data]
                 I [use pI information in PeptideProphet]
                 R [use Hydrophobicity / RT information in PeptideProphet]
                 F [force the fitting of the mixture model, bypass automatic mixture model checks]
                 A [use accurate mass binning in PeptideProphet]
                 w [warning instead of exit with error if instrument types between runs is different]
                 x [exclude all entries with asterisked score values in PeptideProphet]
                 l [leave alone all entries with asterisked score values in PeptideProphet]
                 n [use hardcoded default initialization parameters of the distributions]
                 P [use Non-parametric model, can only be used with decoy option]
                 N [do not use the NTT model]
                 M [do not use the NMC model]
                 k [do not use the mass model]
                 o [optimize f-value function f(dot,delta) using PCA (applies only to SpectraST)]
                 G [use Gamma Distribution to model the Negatives (applies only to X!Tandem data)]
                 E [only use Expect Score as the Discriminant(applies only to X!Tandem data,
                    helpful for data with homologous top hits e.g. phospho or glyco)]
                 d [report decoy hits with a computed probability based on the model learned]
                 p [run ProteinProphet afterwards]
                 t [do not create png data plot]
                 u [do not assemble protein groups in ProteinProphet analysis]
                 s [do not use Occam's Razor in ProteinProphet analysis to
                    derive the simplest protein list to explain observed peptides]

Note: Confirmed that according to the TPP 5.0 release notes that it was removed due to the default behavior being changed to not have the plotting turned on in ProteinProphet:

http://tools.proteomecenter.org/wiki/index.php?title=TPP:5.0.0_Release_Notes

"Stop plotting sens/err png by default; removed NOPLOT option. To produce png, use new PLOTPNG option."

Update: Sent notice to SPC to have them update xinteract to remove the "t" option. Trying to determine whether we can not trigger the "t" option and if so, what will happen.

Bug https://www.labkey.org/home/Developer/issues/issues-details.view?issueId=32442 created on this to update our Java code.

We may need to do more than one update though since xinteract is going to need to be revised to work with ProteinProphet's change with the NOPLOT removal.

Hi Toan,

The upcoming version of LabKey 18.1, you can set the "pipeline tpp, version" parameter to "5" in either the job or the default settings to omit the "t" option.

This should now anticipate using TPP 5.0 or higher, although I've confirmed that TPP 5.2 will make the necessary change to where adjusts for the "t" option as well.

Regards,

Jon