pacmass: Predict the elemental composition of proteins and peptides

In jclaesen/pacMASS-R: Predicting the Elemental Composition of Peptides and Small Proteins Based on the Monoisotopic Mass

Description

Predict the elemental composition of proteins and peptides

Usage

pacmass(mz = NULL, z = NULL, fileNAME = NULL, nbS, ppm = 5, alpha = 0.05)

Arguments

mz	monoisotopic mass-to-charge value
z	charge
fileNAME	name of a file containing mz and z.
nbS	number of S-atoms
ppm	mass error tolerance
alpha	significance level

Details

The default value of mz, and fileNAME is NULL. However one of these parameters has to be defined in order for pacmass to work.

When mz is defined and z=NULL, it is assumed that mz is the mass of a neutral molecule.

When fileNAME is defined, the file has to be a comma-separated (csv) file, a tab-separated txt file or a tab-separated tsv file. The mass values have to be in a column with as name 'mz', the charges have to be in column with as name 'z'.

Value

A list with the predicted elemental compositions

Examples

pacmass(mz=1709.897, nbS=0, ppm=10, alpha=0.05)
pacmass(mz=855.956, z=2, nbS=0)
pacmass(mz=855.956, z=2, nbS=c(0,1))
pacmass(mz=c(855.956,735.693), z=c(2,3), nbS=0)

jclaesen/pacMASS-R documentation built on Jan. 3, 2020, 12:13 a.m.