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MSnID

MSnID is an R/Bioconductor package that provides convience tools for handling and filtering of MS/MS identification results. The official page is the Bioconductor landing page (release or devel versions). The github page page is for sharing, testing, issue tracking and forking/pulling purposes.

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Version

Version

1.6.0

License

Artistic-2.0

Maintainer

Vlad Petyuk

Last Published

February 15th, 2017

Functions in MSnID (1.6.0)

assess_missed_cleavages

Counts the missing cleavage sites within the peptides sequence
MSnID-package

MSnID: Utilities for Handling MS/MS Identifications
id_quality

Identification quality
apply_filter

Filters the MS/MS identifications
recalibrate

Post-experimental recalibration of observed mass to charge ratios
peptides

Non-redundant list of peptides
read_mzIDs

Populates MS/MS results table from mzIdentML files
psms

Peptide-to-spectrum matches
correct_peak_selection

Corrects wrong selection of monoisotopic peak
mass_measurement_error

Computes error of the parent ion mass to charge measurement
MSnID-class

The "MSnID" Class for Mass Spectrometry Based Proteomics Identification Data
optimize_filter

Filter criteria optimization to maximize the number of identifications given the FDR upper threshold
accessions

Non-redundant list of accession (protein) identifiers
MSnIDFilter-class

The "MSnIDFilter" Class for Handling MS/MS Criteria, Relationships and Thresholds for Data Filtration.
evaluate_filter

Filters the MS/MS identifications
assess_termini

Checks if the peptide termini conforms with cleavage specificity
msnidObj

Example mzIdenML File and MSnID Object