parsemsf (version 0.1.1)

make_area_table: Make a table of peptide areas

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

# NOT RUN {
make_area_table(parsemsf_example("test_db.msf"))
# }