Header

UZH-Logo

Maintenance Infos

rawDiag - an R package supporting rational LC-MS method optimization for bottom-up proteomics


Trachsel, Christian; Panse, Christian; Kockmann, Tobias; Wolski, Witold Eryk; Grossmann, Jonas; Schlapbach, Ralph (2018). rawDiag - an R package supporting rational LC-MS method optimization for bottom-up proteomics. bioRxiv 304485, University of Zurich.

Abstract

Optimizing methods for liquid chromatography coupled to mass spectrometry (LC-MS) is a non-trivial task. Here we present rawDiag, a software tool supporting rational method optimization by providing MS operator-tailored diagnostic plots of scan level metadata. rawDiag is implemented as R package and can be executed on the command line, or through a graphical user interface (GUI) for less experienced users. The code runs platform independent and can process a hundred raw files in less than three minutes on current consumer hardware as we show by our benchmark. In order to demonstrate the functionality of our package, we included a real-world example taken from our daily core facility business. The R package itself, a shiny demo application, and a Dockerfile that builds the entire architecture from scratch is accessible through a GitHub repository, see https://github.com/protViz/rawDiag

Abstract

Optimizing methods for liquid chromatography coupled to mass spectrometry (LC-MS) is a non-trivial task. Here we present rawDiag, a software tool supporting rational method optimization by providing MS operator-tailored diagnostic plots of scan level metadata. rawDiag is implemented as R package and can be executed on the command line, or through a graphical user interface (GUI) for less experienced users. The code runs platform independent and can process a hundred raw files in less than three minutes on current consumer hardware as we show by our benchmark. In order to demonstrate the functionality of our package, we included a real-world example taken from our daily core facility business. The R package itself, a shiny demo application, and a Dockerfile that builds the entire architecture from scratch is accessible through a GitHub repository, see https://github.com/protViz/rawDiag

Statistics

Citations

Dimensions.ai Metrics

1 citation in ScopusĀ®

Altmetrics

Downloads

2 downloads since deposited on 05 Mar 2019
2 downloads since 12 months
Detailed statistics

Additional indexing

Item Type:Working Paper
Communities & Collections:04 Faculty of Medicine > Functional Genomics Center Zurich
Dewey Decimal Classification:570 Life sciences; biology
610 Medicine & health
Language:English
Date:2018
Deposited On:05 Mar 2019 15:23
Last Modified:06 Mar 2019 08:33
Series Name:bioRxiv
Additional Information:Now published in Journal of Proteome Research doi: 10.1021/acs.jproteome.8b00173
OA Status:Hybrid
Publisher DOI:https://doi.org/10.1101/304485

Download

Download PDF  'rawDiag - an R package supporting rational LC-MS method optimization for bottom-up proteomics'.
Preview
Content: Accepted Version
Filetype: PDF
Size: 1MB
View at publisher