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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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Updated: Jun 16, 2026

Navigating the Mass Spectrometry-Based Proteomic Data Using Free Computational Tools

Navigating the Mass Spectrometry-Based Proteomic Data Using Free Computational Tools

Published on: August 19, 2025

Skyline: an open source document editor for creating and analyzing targeted proteomics experiments.

Brendan MacLean¹, Daniela M Tomazela, Nicholas Shulman

¹Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA. brendanx@u.washington.edu

Bioinformatics (Oxford, England)

|February 12, 2010

Summary

This summary is machine-generated.

Skyline is a free, open-source Windows application for targeted proteomics. It simplifies mass spectrometry method development and quantitative data analysis using selected reaction monitoring (SRM).

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Area of Science:

Proteomics
Mass Spectrometry
Bioinformatics

Background:

Skyline offers a user-friendly interface for targeted proteomics.
It is freely available for academic and commercial use with web installation and support resources.

Purpose of the Study:

To introduce Skyline as a comprehensive tool for targeted proteomics.
To detail its capabilities in method creation, data analysis, and result visualization.

Main Methods:

Utilizes selected reaction monitoring (SRM) for targeted proteomics.
Supports MS/MS spectral library creation and utilization.
Integrates with major instrument vendor data formats (Agilent, Thermo Fisher, Waters, Applied Biosystems).

Main Results:

Simplifies mass spectrometer method development and data analysis.
Facilitates verification of results using spectral libraries.
Enables seamless data integration from instrument output to experimental design.

Conclusions:

Skyline is an open-source Windows application for targeted proteomics.
It streamlines method creation, quantitative data analysis, and data integrity checks.
Offers powerful visualization and data export for in-depth analysis.