map_peptides: Map peptides to their locations within a protein

In benjaminjack/parsemsf: Parse ThermoFisher MSF Files and Estimate Protein Abundances

Description

Takes a ThermoFisher MSF file and finds the location of each peptide within its corresponding protein sequence. In cases where a single peptide maps to multiple locations within a protein sequence, only the first location is reported. If a peptide maps ambiguously to multiple proteins, all locations are reported with data from each peptide-protein combination on a separate row.

Usage

map_peptides(msf_file, min_conf = "High", prot_regex = "")

Arguments

msf_file	A file path to a ThermoFisher MSF file.
min_conf	"High", "Medium", or "Low". The minimum peptide confidence level to retrieve from MSF file.
prot_regex	Regular expression where the first group matches a protein name or ID from the protein description. Regex must contain ONE group. The protein description is typically generated from a fasta reference file that was used for the database search.

Value

A dataframe containing start and stop positions (relative to the parent protein sequence) for each peptide in the database.

peptide_id	a unique peptide ID
spectrum_id	a unique spectrum ID
protein_id	unique protein group ID to which this peptide maps
protein_desc	protein description from reference database used to assign peptides to protein groups, parsed according to prot_regex
peptide_sequence	amino acid sequence (does not show post-translational modifications)
pep_score	PEP score
q_value	Q-value score
protein_sequence	parent protein sequence
start	start position of peptide within protein sequence
end	end position of peptide within protein sequence

Examples

map_peptides(parsemsf_example("test_db.msf"))

benjaminjack/parsemsf documentation built on May 12, 2019, 11:54 a.m.