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... |
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 |
fetch_conversion_table | Fetches conversion table form one type of identifiers to... |
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... |
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... |
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 |
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