Credential Features

Version: 1.0

Website

http://pattilab.wustl.edu/software/credential/credential.php

Description

This package is designed to optimise LC-MS workflows where 1000s of features are detected from a single run. It uses credentialling to identify features which are artificial as opposed to those of biological origin. To do this E.coli were grown on either natural abundance media or uniformly C13 (UC13) media. These two media were then mixed at different ratios (1:1 and 1:2). Once LC-MS analysis has then be performed. The credential features package is used for data analysis. XCMS and CAMERA are utilized for preprocessing and annotation respectively. The credential features algorithm performs two rounds of filtering to identify biological features. Firstly, coeluting peaks within a single sample are assessed for potential isotopologue pairs and the ratios of 12C:13C are then evaluated and those that are not within a set percentage are discarded. The samples with different ratios of C12:C13 are then taken together for a second round of filtering.

Functionality

• Other Tools/Experimental Optimisation

Instrument Data Type

• MS/LC-MS

Approaches

• Untargeted

Computer Skills

Advanced

Software Type

R Package

Interface

Command line interface

Operating System (OS)

• Unix/Linux
• Mac OS
• Windows

Language

R

Dependencies

xcms, data.table, plyr, CAMERA, ggplot2, gridExtra, Hmisc

Input Formats - Open

Input Formats - Proprietary

Published

2014

Last Updated

2015

License

Paper

http://www.ncbi.nlm.nih.gov/pubmed/25160088

PMID

25160088