parsemsf (version 0.1.1)

make_pep_table: Make a data frame of peptides

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

# NOT RUN {
# 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 = "^(.+)$")

# }