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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 proteomics...

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Selected Reaction Monitoring Mass Spectrometry for Absolute Protein Quantification

Selected Reaction Monitoring Mass Spectrometry for Absolute Protein Quantification

Published on: August 17, 2015

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, WA, USA.

Biorxiv : the Preprint Server for Biology

|April 8, 2025

Summary

QuickProt offers user-friendly Python notebooks for analyzing mass spectrometry (MS) proteomics data. This tool streamlines data interpretation, revealing dynamic proteome changes during human erythropoiesis.

Keywords:

Data-independent acquisition QuickProt erythropoiesis liquid chromatography-tandem mass spectrometry mass spectrometry parallel reaction monitoring proteomics stable isotope dilution

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Last Updated: Jun 4, 2026

Selected Reaction Monitoring Mass Spectrometry for Absolute Protein Quantification

Selected Reaction Monitoring Mass Spectrometry for Absolute Protein Quantification

Published on: August 17, 2015

Mass Spectrometry-Based Proteomics Analyses Using the OpenProt Database to Unveil Novel Proteins Translated from Non-Canonical Open Reading Frames

Mass Spectrometry-Based Proteomics Analyses Using the OpenProt Database to Unveil Novel Proteins Translated from Non-Canonical Open Reading Frames

Published on: April 11, 2019

Simultaneous Affinity Enrichment of Two Post-Translational Modifications for Quantification and Site Localization

Simultaneous Affinity Enrichment of Two Post-Translational Modifications for Quantification and Site Localization

Published on: February 27, 2020

Area of Science:

Proteomics
Biotechnology
Computational Biology

Background:

Mass spectrometry (MS)-based proteomics is crucial for identifying and quantifying biological samples.
Existing software platforms handle raw data processing, but downstream analysis, quality control, and interpretation remain challenging.
Integrated tools for comprehensive proteomics data analysis are lacking.

Purpose of the Study:

To develop an integrated, user-friendly tool for analyzing data-independent acquisition (DIA) and parallel reaction monitoring (PRM) proteomics datasets.
To provide open-source Python-based Google Colab notebooks for streamlined proteomics data analysis.
To facilitate downstream analysis, including quality control, visualization, and interpretation of proteomics results.

Main Methods:

Development of QuickProt, a series of Python-based Google Colab notebooks.
Utilized notebooks for analyzing in-house DIA and stable isotope dilution (SID)-PRM MS proteomics datasets.
Applied notebooks to a time-course study of human erythropoiesis.

Main Results:

QuickProt successfully analyzed DIA and SID-PRM MS proteomics datasets.
Generated annotated tables and publication-ready figures.
Revealed dynamic proteome rearrangement during erythroid differentiation, with increased abundance of proteins in gene regulation, metabolic, and chromatin remodeling pathways.

Conclusions:

QuickProt automates and streamlines DIA and PRM-MS proteomics data analysis.
The tool enhances efficiency and reduces analysis time for researchers.
QuickProt empowers users with limited coding expertise to perform complex proteomics data analysis.