parse_msgf_mzid: Parses a mzID file generated by MS-GF+.

In compomics/search-all-assess-subset: An implementation of the Search All, Asses Subset strategy for FDR estimation shotgun proteomics.

Description

See https://omics.pnl.gov/software/ms-gf for more info on how to perform a database search on MSMS dataset with MS-GF+ and how to generate a mzID file. Note that most functions in these package require data from a competitive target decoy search.

Usage

parse_msgf_mzid(mzid_path)

Arguments

mzid_path

Location of the mzID file.

Details

We take the MS-GF+ SpecEValue as the PSM score for FDR calculation.

Value

A data frame containing the following 7 columns:

spec_id

Id of the spectrum from the searched dataset file.

sequence

Amino acid sequence matching the spectra.

protein_id

Id of the sequence from the database file.

score

score assigned to the peptide to spectrum match (PSM).

database

Name of the database file used to search the spectra.

decoy

TRUE if decoy PSM, FALSE otherwise.

database_size

Number of sequences in the database file.

Examples

## Location of the zipped data files
zip_file_path = system.file("extdata", "extdata.zip", package = "saas")

## Unzip and get the (temporary) location of the mzid file with the MS-GF+ search results from a
## competitive target decoy search of the complete pyrococcus proteome against a pyrococcus dataset.
mzid_file_path = unzip(zip_file_path, 'pyrococcus.mzid',exdir = tempdir())
## Parse the mzid file
parse_msgf_mzid(mzid_file_path)

compomics/search-all-assess-subset documentation built on May 13, 2019, 9:55 p.m.