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

Documentation for package ‘MSnID’ version 1.21.0

DESCRIPTION file.
User guides, package vignettes and other documentation.
Code demos. Use demo() to run them.
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MSnID-package	MSnID: Utilities for Handling MS/MS Identifications
$-method	The "MSnID" Class for Mass Spectrometry Based Proteomics Identification Data
$-method	The "MSnIDFilter" Class for Handling MS/MS Criteria, Relationships and Thresholds for Data Filtration.
$<--method	The "MSnID" Class for Mass Spectrometry Based Proteomics Identification Data
$<--method	The "MSnIDFilter" Class for Handling MS/MS Criteria, Relationships and Thresholds for Data Filtration.
accessions	Non-redundant list of accession (protein) identifiers
accessions-method	The "MSnID" Class for Mass Spectrometry Based Proteomics Identification Data
apply_filter	Filters the MS/MS identifications
apply_filter-method	Filters the MS/MS identifications
as.numeric-method	The "MSnIDFilter" Class for Handling MS/MS Criteria, Relationships and Thresholds for Data Filtration.
assess_missed_cleavages	Counts the missing cleavage sites within the peptides sequence
assess_missed_cleavages-method	The "MSnID" Class for Mass Spectrometry Based Proteomics Identification Data
assess_termini	Checks if the peptide termini conforms with cleavage specificity
assess_termini-method	The "MSnID" Class for Mass Spectrometry Based Proteomics Identification Data
class:MSnID	The "MSnID" Class for Mass Spectrometry Based Proteomics Identification Data
class:MSnIDFilter	The "MSnIDFilter" Class for Handling MS/MS Criteria, Relationships and Thresholds for Data Filtration.
coerce-method	The "MSnID" Class for Mass Spectrometry Based Proteomics Identification Data
correct_peak_selection	Corrects wrong selection of monoisotopic peak
correct_peak_selection-method	The "MSnID" Class for Mass Spectrometry Based Proteomics Identification Data
c_elegans	Example mzIdenML File and MSnID Object
dim-method	The "MSnID" Class for Mass Spectrometry Based Proteomics Identification Data
evaluate_filter	Filters the MS/MS identifications
evaluate_filter-method	The "MSnID" Class for Mass Spectrometry Based Proteomics Identification Data
id_quality	Identification quality
id_quality-method	The "MSnID" Class for Mass Spectrometry Based Proteomics Identification Data
infer_parsimonious_accessions	Eliminates Redundancy in Peptide-to-Protein Mapping
infer_parsimonious_accessions-method	Eliminates Redundancy in Peptide-to-Protein Mapping
length-method	The "MSnIDFilter" Class for Handling MS/MS Criteria, Relationships and Thresholds for Data Filtration.
mass_measurement_error	Computes error of the parent ion mass to charge measurement
mass_measurement_error-method	The "MSnID" Class for Mass Spectrometry Based Proteomics Identification Data
MSnID	The "MSnID" Class for Mass Spectrometry Based Proteomics Identification Data
MSnID-class	The "MSnID" Class for Mass Spectrometry Based Proteomics Identification Data
MSnIDFilter	The "MSnIDFilter" Class for Handling MS/MS Criteria, Relationships and Thresholds for Data Filtration.
MSnIDFilter-class	The "MSnIDFilter" Class for Handling MS/MS Criteria, Relationships and Thresholds for Data Filtration.
msnidObj	Example mzIdenML File and MSnID Object
names-method	The "MSnID" Class for Mass Spectrometry Based Proteomics Identification Data
names-method	The "MSnIDFilter" Class for Handling MS/MS Criteria, Relationships and Thresholds for Data Filtration.
optimize_filter	Filter criteria optimization to maximize the number of identifications given the FDR upper threshold
optimize_filter-method	Filter criteria optimization to maximize the number of identifications given the FDR upper threshold
peptides	Non-redundant list of peptides
peptides-method	The "MSnID" Class for Mass Spectrometry Based Proteomics Identification Data
proteins	Non-redundant list of accession (protein) identifiers
proteins-method	The "MSnID" Class for Mass Spectrometry Based Proteomics Identification Data
psms	Peptide-to-spectrum matches
psms-method	The "MSnID" Class for Mass Spectrometry Based Proteomics Identification Data
psms<-	Peptide-to-spectrum matches
psms<--method	The "MSnID" Class for Mass Spectrometry Based Proteomics Identification Data
read_mzIDs	Populates MS/MS results table from mzIdentML files
read_mzIDs-method	The "MSnID" Class for Mass Spectrometry Based Proteomics Identification Data
recalibrate	Post-experimental recalibration of observed mass to charge ratios
recalibrate-method	The "MSnID" Class for Mass Spectrometry Based Proteomics Identification Data
show-method	The "MSnID" Class for Mass Spectrometry Based Proteomics Identification Data
show-method	The "MSnIDFilter" Class for Handling MS/MS Criteria, Relationships and Thresholds for Data Filtration.
update-method	The "MSnIDFilter" Class for Handling MS/MS Criteria, Relationships and Thresholds for Data Filtration.
[[-method	The "MSnID" Class for Mass Spectrometry Based Proteomics Identification Data
[[<--method	The "MSnID" Class for Mass Spectrometry Based Proteomics Identification Data