README.md

In davidsbutcher/abundancer: Determine Abundances of 12C and 14N from Protein Mass Spectra

Abundancer

Abundancer is used to estimate the isotopic abundances of 12C and 14N from a peaklist of a single charge state of an intact protein and its sequence. This is useful in cases where the abundances of these isotopes are expected to deviate from typical values, e.g. in cases where proteins are isotopically depleted.

Installation

Install from GitHub:

remotes::install_github("davidsbutcher/abundancer")

Usage

To use abundancer, see documentation for calculate_score_matrix_dual().

Arguments for calculate_score_matrix_dual():

• MSspectrum: Input peaklist as an MSnbase Spectrum1 object. If not proved, mz and intensity arguments must be provided.
• mz: Numeric vector of peaklist mz values. Must be same length as intensity.
• intensity: Numeric vector of peaklist intensity values. Must be same length as mz.
• sequence: Character vector of single-letter canonical amino acids.
• PTMformula Character vector containing summary difference formula for any PTMs on the protein in Hill notation, e.g. “C1H2” for methylation.
• charge: Charge state og the protein represented by the peaklist.
• resolvingPower: Resolving power at 400 m/z for the spectrum. Defaults to 300,000, which is typical for 21 T FT-ICR MS data.

Other functions like calculate_score_array() are also available, but under heavy development and not recommended for use.

A Shiny web application for abundancer is hosted at the MagLab ICR group’s TDP apps site. A Docker image of the web application is also available.

davidsbutcher/abundancer documentation built on Feb. 21, 2022, 2:13 p.m.