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

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.

Author
Vlad Petyuk with contributions from Laurent Gatto
Date of publication
None
Maintainer
Vlad Petyuk <petyuk@gmail.com>
License
Artistic-2.0
Version
1.8.0

View on Bioconductor

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...

Files in this package

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