MSnID: Utilities for Exploration and Assessment of Confidence of LC-MSn Proteomics Identifications
Version 1.10.0

Extracts MS/MS ID data from mzIdentML (leveraging mzID package) or text files. After collating the search results from multiple datasets it assesses their identification quality and optimize filtering criteria to achieve the maximum number of identifications while not exceeding a specified false discovery rate. Also contains a number of utilities to explore the MS/MS results and assess missed and irregular enzymatic cleavages, mass measurement accuracy, etc.

AuthorVlad Petyuk with contributions from Laurent Gatto
Bioconductor views MassSpectrometry Proteomics
Date of publicationNone
MaintainerVlad Petyuk <petyuk@gmail.com>
LicenseArtistic-2.0
Version1.10.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("MSnID")

Getting started

Package overview

Popular man pages

apply_filter: Filters the MS/MS identifications
correct_peak_selection: Corrects wrong selection of monoisotopic peak
data: Example mzIdenML File and MSnID Object
id_quality: Identification quality
MSnIDFilter-class: The "MSnIDFilter" Class for Handling MS/MS Criteria,...
MSnID-package: MSnID: Utilities for Handling MS/MS Identifications
peptides: Non-redundant list of peptides
See all...

All man pages Function index File listing

Man pages

accessions: Non-redundant list of accession (protein) identifiers
apply_filter: Filters the MS/MS identifications
assess_missed_cleavages: Counts the missing cleavage sites within the peptides...
assess_termini: Checks if the peptide termini conforms with cleavage...
correct_peak_selection: Corrects wrong selection of monoisotopic peak
data: Example mzIdenML File and MSnID Object
evaluate_filter: Filters the MS/MS identifications
id_quality: Identification quality
infer_parsimonious_accessions: Eliminates Redundancy in Peptide-to-Protein Mapping
mass_measurement_error: Computes error of the parent ion mass to charge measurement
MSnID-class: The "MSnID" Class for Mass Spectrometry Based Proteomics...
MSnIDFilter-class: The "MSnIDFilter" Class for Handling MS/MS Criteria,...
MSnID-package: MSnID: Utilities for Handling MS/MS Identifications
optimize_filter: Filter criteria optimization to maximize the number of...
peptides: Non-redundant list of peptides
psms: Peptide-to-spectrum matches
read_mzIDs: Populates MS/MS results table from mzIdentML files
recalibrate: Post-experimental recalibration of observed mass to charge...

Functions

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/AllClasses.R
R/AllGenerics.R
R/MSnID-methods.R
R/MSnIDFilter-methods.R
R/optimize_filter.r
R/read_mzIDs.R
TODO
build
build/vignette.rds
data
data/c_elegans.RData
demo
demo/00Index
demo/c_elegans.R
inst
inst/doc
inst/doc/msnid_vignette.R
inst/doc/msnid_vignette.Rnw
inst/doc/msnid_vignette.pdf
inst/extdata
inst/extdata/c_elegans.mzid.gz
inst/extdata/human_brain.txt
inst/unitTests
inst/unitTests/test_apply_filter.R
inst/unitTests/test_data_load.R
inst/unitTests/test_infer_parsimonious_accessions.R
inst/unitTests/test_irreg_cleavages.R
inst/unitTests/test_missed_cleavages.R
inst/unitTests/test_optimize_filter.R
man
man/MSnID-class.Rd
man/MSnID-package.Rd
man/MSnIDFilter-class.Rd
man/accessions.Rd
man/apply_filter.Rd
man/assess_missed_cleavages.Rd
man/assess_termini.Rd
man/correct_peak_selection.Rd
man/data.Rd
man/evaluate_filter.Rd
man/id_quality.Rd
man/infer_parsimonious_accessions.Rd
man/mass_measurement_error.Rd
man/optimize_filter.Rd
man/peptides.Rd
man/psms.Rd
man/read_mzIDs.Rd
man/recalibrate.Rd
tests
tests/runTests.R
vignettes
vignettes/msnid.bib
vignettes/msnid_vignette.Rnw
MSnID documentation built on May 20, 2017, 10:41 p.m.

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