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

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Documentation for package ‘MSnID’ version 1.27.0

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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
add_mod_symbol Annotates peptide sequences with modification symbols
add_mod_symbol-method Annotates peptide sequences with modification symbols
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
fetch_conversion_table Fetches conversion table form one type of identifiers to another
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.
map_mod_sites Maps the modifications to protein sequence
map_mod_sites-method Maps the modifications to protein sequence
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
remap_accessions Changes accessions from one protein id to another
remap_accessions-method 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
report_mods-method Lists modification masses in the MSnID object
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