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Proteomics

Proteomics

A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term...

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QuickProt: A Bioinformatics and Visualization Tool for DIA and PRM Mass Spectrometry-Based Proteomics Datasets.

Omar Arias-Gaguancela¹, Carmen Palii², Mehar Un Nissa¹

¹Institute For Systems Biology, Seattle, Washington, USA.

|September 5, 2025

Summary

QuickProt offers user-friendly Google Colab notebooks for analyzing proteomics data from data-independent acquisition (DIA) and parallel reaction monitoring (PRM) mass spectrometry (MS). This tool streamlines analysis, revealing proteome dynamics during human erythropoiesis.

Keywords:

QuickProt data mining and visualization data‐independent acquisition erythropoiesis liquid chromatography‐tandem mass spectrometry mass spectrometry parallel reaction monitoring proteomics stable isotope dilution

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Area of Science:

Proteomics
Mass Spectrometry (MS)
Computational Biology

Background:

Mass spectrometry (MS)-based proteomics is crucial for identifying and quantifying biological peptides and proteins.
Existing software platforms handle raw data processing, but downstream analysis (QC, visualization, interpretation) lacks integrated tools.
This gap hinders efficient and comprehensive proteomics data analysis.

Purpose of the Study:

To develop an integrated, user-friendly software solution for analyzing proteomics data.
To streamline downstream analysis of data-independent acquisition (DIA) and parallel reaction monitoring (PRM) datasets.
To provide accessible tools for researchers with limited coding expertise.

Main Methods:

Development of QuickProt, a suite of Python-based Google Colab notebooks.
Application of QuickProt to analyze in-house DIA and stable isotope dilution (SID)-PRM MS proteomics data.
Utilized a time-course study of human erythropoiesis as a proof-of-concept.

Main Results:

QuickProt successfully analyzed DIA and SID-PRM MS proteomics datasets.
Generated annotated tables and publication-ready figures showcasing proteome dynamics.
Identified early increases in proteins related to gene regulation, metabolism, and chromatin remodeling during erythropoiesis.

Conclusions:

QuickProt effectively automates and streamlines DIA and PRM-MS proteomics data analysis.
The open-source notebooks enhance accessibility and customizability for researchers.
The tool facilitates efficient interpretation of complex proteomics datasets, accelerating scientific discovery.