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

Functions

accessions Man page
accessions,MSnID-method Man page
apply_filter Man page
apply_filter,MSnID,character-method Man page
apply_filter,MSnID,MSnIDFilter-method Man page
as.numeric,MSnIDFilter-method Man page
assess_missed_cleavages Man page
assess_missed_cleavages,MSnID-method Man page
assess_termini Man page
assess_termini,MSnID-method Man page
c_elegans Man page
class:MSnID Man page
class:MSnIDFilter Man page
coerce,MSnID,data.table-method Man page
coerce,MSnID,MSnSet-method Man page
correct_peak_selection Man page
correct_peak_selection,MSnID-method Man page
dim,MSnID-method Man page
evaluate_filter Man page
evaluate_filter,MSnID-method Man page
id_quality Man page
id_quality,MSnID-method Man page
infer_parsimonious_accessions Man page
infer_parsimonious_accessions,MSnID-method Man page
length,MSnIDFilter-method Man page
mass_measurement_error Man page
mass_measurement_error,MSnID-method Man page
MSnID Man page
[[,MSnID,ANY,ANY-method Man page
MSnID-class Man page
MSnIDFilter Man page
MSnIDFilter-class Man page
$<-,MSnIDFilter-method Man page
$,MSnIDFilter-method Man page
[[<-,MSnID-method Man page
[[,MSnID-method Man page
$<-,MSnID-method Man page
$,MSnID-method Man page
msnidObj Man page
MSnID-package Man page
names,MSnIDFilter-method Man page
names,MSnID-method Man page
optimize_filter Man page
optimize_filter,MSnIDFilter,MSnID-method Man page
peptides Man page
peptides,MSnID-method Man page
proteins Man page
proteins,MSnID-method Man page
psms Man page
psms<- Man page
psms<-,MSnID,data.frame-method Man page
psms,MSnID-method Man page
read_mzIDs Man page
read_mzIDs,MSnID-method Man page
recalibrate Man page
recalibrate,MSnID-method Man page
show,MSnIDFilter-method Man page
show,MSnID-method Man page
update,MSnIDFilter-method Man page

Files

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

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