Abstract
Every laboratory performing mass-spectrometry-based proteomics strives to generate high-quality data. Among the many factors that impact the outcome of any experiment in proteomics is the LC–MS system performance, which should be monitored within each specific experiment and also long term. This process is termed quality control (QC). We present an easy-to-use tool that rapidly produces a visual, HTML-based report that includes the key parameters needed to monitor the LC–MS system performance, with a focus on monitoring the performance within an experiment. The tool, named RawBeans, generates a report for individual files or for a set of samples from a whole experiment. We anticipate that it will help proteomics users and experts evaluate raw data quality independent of data processing. The tool is available at https://bitbucket.org/incpm/prot-qc/downloads. The mass-spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the data set identifier PXD022816.
Highlights
Mass-spectrometry-based proteomics is an essential technique in life sciences, enabling analyses of whole proteomes, posttranslational modifications, protein−protein interactions, and more
The data can be of data-dependent acquisition (DDA) type or data-independent acquisition (DIA) type for Thermo data only (Supplementary File S5)
We developed an easy-to-use tool that provides information regarding the quality of the mass-spectrometry data postacquisition
Summary
Mass-spectrometry-based proteomics is an essential technique in life sciences, enabling analyses of whole proteomes, posttranslational modifications, protein−protein interactions, and more. Two of the earliest tools were RawMeat by Vast Scientific, which is no longer supported, and LogViewer,[17] which requires prepreparation of the data before analysis. Both tools provide quick, identification-free, graphic information about the instrument performance and are simple to use, which is why they were popular; they are limited to Thermo instruments and are not updated to handle the latest instrumentation
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