Parse ThermoFisher MSF Files and Estimate Protein Abundances

Provides functions for parsing ThermoFisher MSF files produced by Proteome Discoverer 1.4.x (see < https://thermofisher.com> for more information). This package makes it easy to view individual peptide information, including peak areas, and to map peptides to locations within the parent protein sequence. This package also estimates protein abundances from peak areas and across multiple technical replicates. The author of this package is not affiliated with ThermoFisher Scientific in any way.


The main purpose of the ParseMSF package is to parse proprietary Thermo MSF files into a format readable by R. This package makes it easy to view individual peptide information, including peak areas, and to map peptides to locations within the parent protein sequence. This package also estimates protein abundances from peak areas and across multiple technical replicates.

Currently, the ParseMSF package provides functions for parsing Thermo MSF files produced by Proteome Discoverer 1.4.x only.

Installation

This latest stable release of this package can be installed from CRAN by running the following command in the R console:

install.packages("parsemsf")

If you want to install the development version this package from Github by running the following command in the R console:

devtools::install_github("benjaminjack/parsemsf")

Usage

To get an introduction to the functions in ParseMSF, please see the Introduction vignette on CRAN.

Acknowledgements

Some of the SQL queries in this package come from the now-defunct paRseMSF package by Ashoka Polpitiya.

News

parsemsf 0.1.1

Added support for dplyr 0.6.0

parsemsf 0.1.0

Initial release

Reference manual

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install.packages("parsemsf")

0.1.1 by Benjamin Jack, 7 months ago


https://github.com/benjaminjack/parsemsf/


Report a bug at https://github.com/benjaminjack/parsemsf/issues


Browse source code at https://github.com/cran/parsemsf


Authors: Benjamin Jack [aut, cre]


Documentation:   PDF Manual  


GPL-2 license


Imports dplyr, dbplyr, DBI, lazyeval, RSQLite, stats, stringr, tidyr

Suggests testthat, knitr, rmarkdown, ggplot2


See at CRAN