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 <email@example.com>|
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...