make_area_table: Make a table of peptide areas

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

Description

Areas under each peptide peak that can be used downstream for quantitation. See quantitate for protein quantitation.

Usage

make_area_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 containing peptide areas for peptides at or above the minimum confidence level.

peptide_id	a unique peptide ID
spectrum_id	a unique spectrum ID
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)
area	area under peptide peak
mass	peptide mass
m_z	mass-to-charge ratio
charge	peptide charge
intensity	peak intensity; useful if no area is available
first_scan	first scan in which peptide appears

Examples

make_area_table(parsemsf_example("test_db.msf"))

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