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ProteinProphet
Statistical validation of protein identification based on peptide assignment to MS/MS spectra
ProteinProphet v5.01
philosopher proteinprophet [flags] [files]
--accuracy
Equivalent to MINPROB0.
--allpeps
Consider all possible peptides in the database in the confidence model.
--asap
Compute ASAP ratios for protein entries (ASAP must have been run previously on interact dataset).
--asapprophet
Compute ASAP ratios for protein entries (ASAP must have been run previously on all input interact datasets with mz/XML raw data format).
--confem
Use the EM to compute probability given the confidence.
--delude
Do NOT use peptide degeneracy information when assessing proteins.
--maxppmdiff
Maximum peptide mass difference in PPM (default 20)
--fpkm
Model protein FPKM values.
--glyc
Highlight peptide N-glycosylation motif.
--icat
Highlight peptide cysteines.
--instances
Use Expected Number of Ion Instances to adjust the peptide probabilities prior to NSP adjustment.
--iprophet
Input is from iProphet.
--logprobs
Use the log of the probabilities in the Confidence calculations.
--minindep
Minimum percentage of independent peptides required for a protein (default=0).
--minprob
PeptideProphet probability threshold (default=0.05).
--mufactor
Fudge factor to scale MU calculation (default 1).
--nogroupwts
Check peptide's Protein weight against the threshold (default: check peptide's Protein Group weight against threshold).
--nooccam
Non-conservative maximum protein list.
--noprotlen
Do not report protein length.
--normprotlen
Normalize NSP using Protein Length.
--output
Output name (default "interact.prot.xml").
--protmw
Get protein mol weights.
--refresh
Import manual changes to AAP ratios (after initially using ASAP option).
--softoccam
Peptide weights are apportioned equally among proteins within each Protein Group (less conservative protein count estimate).
--unmapped
Report results for UNMAPPED proteins.
Execute a standard analysis on a pepXML file called sample.pepxml.
philosopher proteinprophet sample.pepxml
Do I need TPP installed for running this ?
No