accessions              Non-redundant list of accession (protein)
                        identifiers
add_mod_symbol          Annotates peptide sequences with modification
                        symbols
apply_filter            Filters the MS/MS identifications
assess_missed_cleavages
                        Counts the missing cleavage sites within the
                        peptides sequence
assess_termini          Checks if the peptide termini conforms with
                        cleavage specificity
correct_peak_selection
                        Corrects wrong selection of monoisotopic peak
evaluate_filter         Filters the MS/MS identifications
fetch_conversion_table
                        Fetches conversion table form one type of
                        identifiers to another
id_quality              Identification quality
infer_parsimonious_accessions
                        Eliminates Redundancy in Peptide-to-Protein
                        Mapping
map_mod_sites           Maps the modifications to protein sequence
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
MSnID-package           MSnID: Utilities for Handling MS/MS
                        Identifications
MSnIDFilter-class       The "MSnIDFilter" Class for Handling MS/MS
                        Criteria, Relationships and Thresholds for Data
                        Filtration.
msnidObj                Example mzIdenML File and MSnID Object
optimize_filter         Filter criteria optimization to maximize the
                        number of identifications given the FDR upper
                        threshold
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 ratios
remap_accessions        Changes accessions from one protein id to
                        another
remap_fasta_entry_names
                        Remapping entries in FASTA file
report_mods             Lists modification masses in the MSnID object
