make_pep_table: Make a data frame of peptides

In parsemsf: Parse ThermoFisher MSF Files and Estimate Protein Abundances

Description

Extracts amino acid sequences (without post-translational modifications), assigned protein groups, and quality scores.

Usage

make_pep_table(msf_file, min_conf = "High",
  prot_regex = "^>([a-zA-Z0-9._]+)\\b", collapse = TRUE)

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.
collapse	If TRUE, peptides that match to multiple protein sequences are collapsed into a single row with multiple protein descriptions and protein IDs in the Proteins and ProteinID columns separated by semi-colons (";").

Value

A data frame of all peptides above the confidence cut-off from a ThermoFisher MSF file.

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
sequence	amino acid sequence (does not show post-translational modifications)
pep_score	PEP score
q_value	Q-value score

Examples

# Read from a path

make_pep_table(parsemsf_example("test_db.msf"))

# Retrieve full protein description

make_pep_table(parsemsf_example("test_db.msf"), prot_regex = "")

# ...which is also equivalent to...

make_pep_table(parsemsf_example("test_db.msf"), prot_regex = "^(.+)$")

parsemsf documentation built on May 2, 2019, 6:33 a.m.