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.

AuthorVlad Petyuk with contributions from Laurent Gatto
Date of publicationNone
MaintainerVlad Petyuk <petyuk@gmail.com>
LicenseArtistic-2.0
Version1.8.0

View on Bioconductor

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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