parsemsf (version 0.1.1)

quantitate: Combine technical replicates and quantitate proteins

Description

Takes a list of thermo MSF files, parses and combines them into a single data frame, and computes areas for each protein group based on the top 3 method of quantitation.

Usage

quantitate(reps, normalize = T, match_peps = T, relabel = c())

Arguments

reps

Vector. List of thermo MSF file names

normalize

Boolean. Should we normalize peptide areas for technical replicate to the total areas in a given replicate?

match_peps

Boolean. Should we quantitate only on matching peptides across technical replicates?

relabel

Named vector for relabeling protein groups. Names correspond to a pattern or string to match (i.e. the name or ID of a protein group), and values correspond to the new value (i.e. new protein group name).

Value

A data frame containing area information for all proteins.

protein_desc

protein description

area_mean

average peptide area

area_sd

peptide area standard deviation

peps_per_rep

Number of peptides per technical replicate used to calculate area_mean and area_sd. This is typically 3 peptides, but may be less.

Examples

# NOT RUN {
quantitate(c(parsemsf_example("test_db.msf"),
             parsemsf_example("test_db2.msf")),
           relabel = c("NP_12345.1" = "NP_1000.1"))
# }