Recent Advances in Mass Spectrometry-Based Bottom-Up Proteomics

Cameron S Movassaghi^{1

2

3}, Jie Sun⁴, Yuming Jiang^{1

2

3}, Natalie Turner⁵, Vincent Chang⁶, Nara Chung⁶, Ryan J Chen⁶, Elizabeth N Browne⁶, Chuwei Lin⁷, Devin K Schweppe⁷, Stacy A Malaker⁶, Jesse G Meyer^{1

2

3}

Affiliations

¹ Department of Computational Biomedicine, Cedars Sinai Medical Center, Los Angeles, California 90048, United States.
² Advanced Clinical Biosystems Research Institute, Cedars Sinai Medical Center, Los Angeles, California 90048, United States.
³ Smidt Heart Institute, Cedars Sinai Medical Center, Los Angeles, California 90048, United States.
⁴ Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United States.
⁵ Departments of Molecular Medicine and Neurobiology, Scripps Research Institute, La Jolla, California 92037, United States.
⁶ Department of Chemistry, Yale University, 275 Prospect Street, New Haven, Connecticut 06511, United States.
⁷ Department of Genome Sciences, University of Washington, Seattle, Washington 98105, United States.

PMID: 40000226
PMCID: PMC12117541 (available on 2026-03-11)
DOI: 10.1021/acs.analchem.4c06750

Review

Recent Advances in Mass Spectrometry-Based Bottom-Up Proteomics

Cameron S Movassaghi et al. Anal Chem. 2025.

. 2025 Mar 11;97(9):4728-4749.

doi: 10.1021/acs.analchem.4c06750. Epub 2025 Feb 25.

Authors

Affiliations

¹ Department of Computational Biomedicine, Cedars Sinai Medical Center, Los Angeles, California 90048, United States.
² Advanced Clinical Biosystems Research Institute, Cedars Sinai Medical Center, Los Angeles, California 90048, United States.
³ Smidt Heart Institute, Cedars Sinai Medical Center, Los Angeles, California 90048, United States.
⁴ Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United States.
⁵ Departments of Molecular Medicine and Neurobiology, Scripps Research Institute, La Jolla, California 92037, United States.
⁶ Department of Chemistry, Yale University, 275 Prospect Street, New Haven, Connecticut 06511, United States.
⁷ Department of Genome Sciences, University of Washington, Seattle, Washington 98105, United States.

PMID: 40000226
PMCID: PMC12117541 (available on 2026-03-11)
DOI: 10.1021/acs.analchem.4c06750

Abstract

Mass spectrometry-based proteomics is about 35 years old, and recent progress appears to be speeding up across all subfields. In this review, we focus on advances over the last two years in select areas within bottom-up proteomics, including approaches to high-throughput experiments, data analysis using machine learning, drug discovery, glycoproteomics, extracellular vesicle proteomics, and structural proteomics.

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References

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Recent Advances in Mass Spectrometry-Based Bottom-Up Proteomics

Affiliations

Recent Advances in Mass Spectrometry-Based Bottom-Up Proteomics

Authors

Affiliations

Abstract

References

Publication types

MeSH terms

Grants and funding

LinkOut - more resources

Full Text Sources