Interactive Web Tool for Standardizing Proteomics Workflow for Liquid Chromatography-Mass Spectrometry Data

Area of Science:

• Proteomics
• Bioinformatics
• Computational Biology

Background:

• Proteomics experiments involve multiple steps with numerous choices, necessitating workflow standardization for robust experimental design.
• Quantitative liquid chromatography-mass spectrometry measurements face challenges like technical variability and missing data, impacting data reliability.

Purpose of the Study:

• To introduce a web application, Proteomics Workflow Standardization Tool (PWST), for standardizing proteomics experimental workflows.
• To assist researchers in selecting optimal choices for each experimental step by identifying those with minimal variability.

Main Methods:

• PWST utilizes statistical methods, including general linear models, analysis of covariance, and analysis of variance, to assess variability.
• The tool analyzes data at both protein and peptide levels, accommodating missing values and calculating the Coefficient of Variation (CV).

Main Results:

• Demonstration of PWST on data with categorical and continuous variables, highlighting its utility in variability assessment.
• The application provides options to determine the contribution of sum of squares for each variable and the CV.

Conclusions:

• PWST offers a valuable resource for standardizing proteomics workflows, thereby improving the reliability of quantitative measurements.
• The web application is freely accessible and implemented in R as a Shiny application.