Creation of MsExperiment objects for MsQuality-based QC metric calculation

Data quality assessment is an integral part of preparatory data analysis to ensure sound biological information retrieval.

We present here the MsQualityUtils package, which provides functionality to create MsExperiment objects from mzML and MetIDQ-derived files.

The MsExperiment files can subsequently be used to calculate quality metrics at the per-sample level using the MsQuality package.

MsQuality relies on the mzQC framework of quality metrics defined by the Human Proteome Organization-Proteomics Standards Intitiative (HUPO-PSI).

The MsQuality package is built upon the Spectra and the MsExperiment package. Metrics will be calculated based on the information stored in a Spectra object, thus, the spectral data of each sample should be stored in one Spectra object. The MsExperiment serves as a container to store the mass spectral data of multiple samples. MsQuality enables the user to calculate quality metrics both on Spectra and MsExperiment objects. The MsQualityUtils package provides functionality to create MsExperiment objects that store the (spectral) information of mzML or MetIDQ files.

You are welcome to

• write a mail to <thomasnaake (at) googlemail (dot) com>
• submit suggestions and issues: https://github.com/tnaake/MsQualityUtils/issues
• send a pull request: https://github.com/tnaake/MsQualityUtils/issues

To install MsQualityUtils, you have first to install the devtools package:

install.packages("devtools")
library("devtools")

Install the MsQualityUtils package then via

install_github("tnaake/MsQualityUtils")