Cited by 130Advanced Proteomics Techniques and ApplicationsMass Spectrometry Techniques and ApplicationsMetabolomics and Mass Spectrometry Studies

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Toward an Optimized Workflow for Middle-Down Proteomics

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Cristobal, Alba, Marino, Fabio, Post, Harm, van den Toorn, Henk W. P., Mohammed, Shabaz, Heck, Albert J. R.·2017·Analytical Chemistry

DOI 10.1021/acs.analchem.6b03756PMC PMC5362747

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Abstract

Mass spectrometry (MS)-based proteomics workflows can crudely be classified into two distinct regimes, targeting either relatively small peptides (i.e., 0.7 kDa < Mw < 3.0 kDa) or small to medium sized intact proteins (i.e., 10 kDa < Mw < 30 kDa), respectively, termed bottom-up and top-down proteomics. Recently, a niche has started to be explored covering the analysis of middle-range peptides (i.e., 3.0 kDa < Mw < 10 kDa), aptly termed middle-down proteomics. Although middle-down proteomics can follow, in principle, a modular workflow similar to that of bottom-up proteomics, we hypothesized that each of these modules would benefit from targeted optimization to improve its overall performance in the analysis of middle-range sized peptides. Hence, to generate middle-range sized peptides from cellular lysates, we explored the use of the proteases Asp-N and Glu-C and a nonenzymatic acid induced cleavage. To increase the depth of the proteome, a strong cation exchange (SCX) separation, carefully tuned to improve the separation of longer peptides, combined with reversed phase-liquid chromatography (RP-LC) using columns packed with material possessing a larger pore size, was used. Finally, after evaluating the combination of potentially beneficial MS settings, we also assessed the peptide fragmentation techniques, including higher-energy collision dissociation (HCD), electron-transfer dissociation (ETD), and electron-transfer combined with higher-energy collision dissociation (EThcD), for characterization of middle-range sized peptides. These combined improvements clearly improve the detection and sequence coverage of middle-range peptides and should guide researchers to explore further how middle-down proteomics may lead to an improved proteome coverage, beneficial for, among other things, the enhanced analysis of (co-occurring) post-translational modifications.

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Authors: Cristobal, A., Marino, F., Post, H., van den Toorn, H. W. P., Mohammed, S., & Heck, A. J. R.
Affiliations: Utrecht University (NL)
Utrecht University , , Padualaan 8 , ,
Corresponding author: Mohammed, Shabaz
Heck, Albert J. R.
ORCID: Marino, Fabio
Mohammed, Shabaz
Heck, Albert J. R.
Venue: Analytical Chemistry
Publisher: American Chemical Society (ACS)
Published: 2017-02-24
Volume: 89
Issue: 6
Pages: 3318-3325
ISSN: 0003-2700 (ISSN-L)
1520-6882
DOI: 10.1021/acs.analchem.6b03756
PMC: PMC5362747
OpenAlex: W2590064181
Cited by: 130
References: 62
Citations by year: 2026: 7 · 2025: 17 · 2024: 8 · 2023: 20 · 2022: 8 · 2021: 17 · 2020: 18 · 2019: 17 · 2018: 11 · 2017: 5
FWCI: 6.88
Type: journal article
Language: en
Open access: hybrid
doi.org
Licence: cc-by-nc-nd
pubs.acs.org/page/policy/authorchoice_ccbyncnd_termsofuse.html (vor, 14 d)
Locations: Analytical Chemistry (publishedVersion, cc-by-nc-nd)
PubMed Central (publishedVersion)
PubMed (publishedVersion)
Utrecht University Repository (Utrecht University) (submittedVersion, other-oa)
Funders: Horizon 2020 Framework Programme (686547)
Nederlandse Organisatie voor Wetenschappelijk Onderzoek (184.032.201, 700.10.429, 718.015.003)
Topics: Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
Physical Sciences › Chemistry › Spectroscopy › Mass Spectrometry Techniques and Applications
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Metabolomics and Mass Spectrometry Studies
Keywords: middle-down proteomics, reversed-phase liquid chromatography, electron transfer dissociation, post-translational modification, sequencing depth
MeSH terms: HeLa Cells, Humans, Particle Size, Peptide Hydrolases, Peptides, Mass Spectrometry, Proteomics

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Toward an Optimized Workflow for Middle-Down Proteomics

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