PeptideProphet

Statistical validation of peptide assignments with PeptideProphet

Version

PeptideProphet v5.2.1

Usage

philosopher peptideprophet [flags] [files]

Flags

--accmass

Use Accurate Mass model binning.

--clevel

Set Conservative Level in neg_stdev from the neg_mean, low numbers are less conservative, high numbers are more conservative.

--combine

Combine the results from PeptideProphet into a single result file.

--database

Path to the database file.

--decoy

Semi-supervised mode, protein name prefix to identify Decoy entries ("rev_" by default).

--decoyprobs

Compute possible non-zero probabilities for Decoy entries on the last iteration.

--enzyme

Enzyme used in sample.

--expectscore

Use expectation value as the only contributor to the f-value for modeling.

--glyc

Enable peptide Glyco motif model.

--ignorechg

Can be used multiple times to specify all charge states to exclude from modeling.

--masswidth

Model mass width in Da (default 5.0).

--minpeplen

Minimum peptide length not rejected (default 7).

--minprob

Minimum probability after first pass of a peptide used for positive RT model (default 0.05).

--nomass

Disable mass model.

--nonmc

Disable NMC missed cleavage model.

--nonparam

Use semi-parametric modeling, must be used in conjunction with --decoy option.

--nontt

Disable NTT enzymatic termini model.

--output

Output name prefix (default "interact").

--perfectlib

Multiply by SpectraST library probability.

--phospho

Enable peptide Phospho motif model.

--ppm

Use ppm mass error instead of Dalton for mass modeling.

Example

Process two pepXML files, combining them into a single output called combined_samples. The analysis will compute possible non-zero probabilities for decoy entries using an accurate mass model for binning.

philosopher peptideprophet --database db.fasta --combine --decoyprobs --accmass --nonparam --output combined_samples sample1.pepxml sample2.pepxml

FAQ

Do I need TPP installed for running this ?

No

What other enzymes are supported by PeptideProphet ?

• trypsin : cut(KR) nocuts(P) sense(C)

• stricttrypsin : cut(KR) sense(C)

• argc : cut(R) nocuts(P) sense(C)

• aspn : cut(D) sense(N)

• chymotrypsin : cut(FLWY) nocuts(P) sense(C)

• clostripain : cut(R) nocuts(-) sense(C)

• cnbr : cut(M) sense(C)

• elastase : cut(AGILV) nocuts(P) sense(C)

• formicacid : cut(D) nocuts(P) sense(C)

• gluc : cut(DE) nocuts(P) sense(C)

• gluc_bicarb : cut(E) nocuts(P) sense(C)

• iodosobenzoate : cut(W) nocuts(-) sense(C)

• lysc : cut(K) nocuts(P) sense(C)

• lysc-p : cut(K) sense(C)

• lysn : cut(K) sense(N)

• lysn_promisc : cut(KR) sense(N)

• ralphtrypsin : cut(KRST) nocuts(P) sense(C)

• nonspecific : cut() sense(C)

• pepsina : cut(FL) nocuts(-) sense(C)

• proline_endopeptidase : cut(P) nocuts(-) sense(C)

• trypsin/chymotrypsin : cut(FYWLKR) nocuts(P) sense(C)

• staph_protease : cut(E) nocuts(-) sense(C)

• tca : cut(KR) nocuts(P) sense(C) : cut(YWFM) nocuts(P) sense(C) : cut(D) sense(N)

• trypsin/cnbr : cut(KR) nocuts(P) sense(C)

• trypsin_gluc : cut(DEKR) nocuts(P) sense(C)

• trypsin_k : cut(K) nocuts(P) sense(C)

• trypsin_r : cut(R) nocuts(P) sense(C)

• thermolysin : cut(ALIVFM) nocuts(DE) sense(N)