Cited by 507Advanced Proteomics Techniques and ApplicationsMass Spectrometry Techniques and ApplicationsMetabolomics and Mass Spectrometry Studies

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Top Down proteomics: Facts and perspectives

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Catherman, Adam D., Skinner, Owen S., Kelleher, Neil L.·2014·Biochemical and Biophysical Research Communications

DOI 10.1016/j.bbrc.2014.02.041PMC PMC4103433

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Abstract

The rise of the "Top Down" method in the field of mass spectrometry-based proteomics has ushered in a new age of promise and challenge for the characterization and identification of proteins. Injecting intact proteins into the mass spectrometer allows for better characterization of post-translational modifications and avoids several of the serious "inference" problems associated with peptide-based proteomics. However, successful implementation of a Top Down approach to endogenous or other biologically relevant samples often requires the use of one or more forms of separation prior to mass spectrometric analysis, which have only begun to mature for whole protein MS. Recent advances in instrumentation have been used in conjunction with new ion fragmentation using photons and electrons that allow for better (and often complete) protein characterization on cases simply not tractable even just a few years ago. Finally, the use of native electrospray mass spectrometry has shown great promise for the identification and characterization of whole protein complexes in the 100 kDa to 1 MDa regime, with prospects for complete compositional analysis for endogenous protein assemblies a viable goal over the coming few years.

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Suddull, H., Rosa-Fernandes, L., & Lee, A. (2023) · Espert Review of Proteomics · doi:10.1080/14789450.2023.2240513 · Cited by 1
Perspective on the potential of tandem-ion mobility/mass spectrometry methods for structural proteomics applications
Cropley, T. C., Chai, M., Liu, F. C., & Bleiholder, C. (2023) · Frontiers in Analytical Science · doi:10.3389/frans.2023.1106752 · Cited by 1
“Mass spectrometry-based methods have proven particularly successful in identifying and quantifying the constituent proteins of proteomes, including different molecular forms of a protein (“proteoforms”) produced via mechanisms such as alternative splicing of transcripts and posttranslational modification of proteins (…”
Method
Fast detection of isocarbophos using bis-propargylcalix[4]arene-stabilized silver nanoparticles
Hu, H., Liu, Z., Li, G., Hu, H.-L., Qu, Y., Lu, Z.-Y., Lu, M., Liang, F., & Li, H.-B. (2022) · Analytical Sciences · doi:10.1007/s44211-022-00102-w · Cited by 1
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Gagaoua, M., Terlouw, C. E. M., & Picard, B. B. (2021) · INRAE Productions Animales · doi:10.20870/productions-animales.2021.34.3.4899 · Cited by 3
Extending the mass-to-charge scannable range of a linear ion trap mass spectrometer through quadrupolar direct current scan
Zhang, D., Jiang, Y., Chu, S., Dai, X., & Fang, X. (2021) · International Journal of Mass Spectrometry · doi:10.1016/j.ijms.2021.116760 · Cited by 2
Challenges and limitations in the studies of glycoproteins: A computational chemist's perspective
Balli, O. I., Uversky, V. N., Durdağı, S., & Coskuner‐Weber, O. (2021) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.26242 · Cited by 2
“In top-down proteomics methods—unlike bottom-up proteomics methods—the aim is to determine the structure by ionization without deteriorating the protein structure.(45) Such methods are reported to”
Method
FBPAII and rpoBC, the Two Novel Secreted Proteins Identified by the Proteomic Approach from a Comparative Study between Antibiotic-Sensitive and Antibiotic-Resistant Helicobacter pylori-Associated Gastritis Strains
Kittisenachai, S., Rojpibulstit, P., Vilaichone, R., Gamnarai, P., Phaonakrop, N., & Suealek, N. (2021) · Infection and Immunity · doi:10.1128/iai.00053-21 · Cited by 2
Mass spectrometric investigations of caloric restriction mimetics
Bibyk, M. J., Campbell, M. J., & Hummon, A. B. (2021) · PROTEOMICS · doi:10.1002/pmic.202000121 · Cited by 1
Approaching complexity: systems biology and ms-based techniques to address immune signaling
Gillen, J., Bridgwater, C., & Nita‐Lazar, A. (2020) · Expert Review of Proteomics · doi:10.1080/14789450.2020.1780920 · Cited by 2
Proteoforms: General Concepts and Methodological Process for Identification
Araújo, J. D. S., & Machado, O. L. T. (2020) · IntechOpen eBooks · doi:10.5772/intechopen.89914 · Cited by 2
Développements méthodologiques en protéomique quantitative pour mieux comprendre la biologie évolutive d'espèces non séquencées
Benhaim-Delarbre, M. (2017) · theses.fr (ABES) · doi:10.70675/58b7965dzfdc5z4cf6zb345z2391827f2628
“Et enfin, la dernière approche, appelée « top-down » [11] consiste à analyser les protéines entières.”
Mass graphs and their applications in top-down proteomicsPreprint
Kou, Q., Wu, S., Tolić, N., Paša‐Tolić, L., & Liu, X. (2015) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/031997 · Cited by 1
“Top-down mass spectrometry (MS) has unique advantages in identifying proteoforms with multiple PSAs because it analyzes intact proteoforms rather than short peptides [4, 20, 22].”
Background
Bioinformatics Approaches for Fungal Biotechnology
Li, J., de Vries, R. P., & Peng, M. (2020) · Elsevier eBooks · doi:10.1016/b978-0-12-819990-9.00012-3 · Cited by 2
Proteomics and Biological Evaluation of Marshmallow (Althea Proteomics and Biological Evaluation of Marshmallow (Althea officinalis) Seeds officinalis) Seeds Proteomics and Biological Evaluation of Marshmallow ( Althea officinalis) Seeds Proteomics and Biological Evaluation of Marshmallow ( Althea o
Amini, M. (2020) · doi:10.36837/chapman.000091 · Cited by 1
“(Catherman et al., 2014).”
Prospects of translational proteomics and protein microarrays in oligodendroglioma
Gupta, S., & Srivastava, S. (2019) · Oligodendroglioma · doi:10.1016/b978-0-12-813158-9.00010-4 · Cited by 1
A method of GC-MS analysis of serum metabolites
Soheili, M., Oskuei, A. A., Tavirani, M., Banitaba, S., Aliakbarzadeh, G., & Salami, M. (2018) · doi:10.22037/jps.v9i1.16927 · Cited by 1
Proteomics, Top-Down
Wu, S., Ma, H., Prytkova, I., Stenoien, D. L., & Paša‐Tolić, L. (2016) · Elsevier eBooks · doi:10.1016/b978-0-12-409547-2.12138-9 · Cited by 2
A Streamlined One-Pot Extraction Method Enables High-Sensitivity Top-Down Proteomic Characterization of Phospholamban from Biopsy-Scale Cardiac Tissue
Clemmer, I. R., Rogers, H. T., Wilson, M. C., Gao, Z., Chan, H., Gregorich, Z. R., Raza, F., & Ge, Y. (2026) · Journal of the American Society for Mass Spectrometry · doi:10.1021/jasms.6c00309
Top-Down Proteomics Analysis of pg-Level Cell Lysate Using Spray-Capillary CE-FAIMS-MS
Anjum, S., Zhao, Z., Cupp‐Sutton, K. A., & Wu, S. (2026) · Journal of Proteome Research · doi:10.1021/acs.jproteome.6c00353
MALDI-Based Multiomics and Spatial Molecular Profiling—Principles, Integrated Workflows, Biomedical Applications, and Future Perspectives: A Systematic Review
Bartusik‐Aebisher, D., Wilk, I., George, B. P. A., & Aebisher, D. (2026) · Biophysica · doi:10.3390/biophysica6050085
Top-Down versus Bottom-Up Proteomics in Highly Sensitive LC-MS-Based Profiling of Limited Samples
Gao, Y., Greguš, M., Kostas, J. C., Marie, A., & Ivanov, A. R. (2026) · Analytical Chemistry · doi:10.1021/acs.analchem.6c01310
Top-Down Sequencing of Intact Proteoforms Using the timsOmni Mass Spectrometer: Accurate Determination of Co-Occurring Histone Modifications
Berthias, F., Bilgin, N., Smyrnakis, A., Boiteux, E. L., Kosmopoulou, M., Albers, C., Suckau, D., Mecinović, J., Papanastasiou, D. K., & Jensen, O. N. (2026) · Molecular & Cellular Proteomics · doi:10.1016/j.mcpro.2026.101640
“Electron-based dissociation methods (ECD/ETD) generate more extensive backbone fragmentation and are particularly suited for large, highly charged protein ions while preserving labile PTMs (45–47).”
Top-Down Mass Spectrometry and Its Current Applications in Biomarker Discovery in Aging and Age-Related Diseases
Lee, E. J., Choi, H., Min, K. H., Park, H. W., & Pack, S. P. (2026) · International Journal of Molecular Sciences · doi:10.3390/ijms27083610
Omic analysis of the protein profile in digestive tumours, from proteomics to clinical practice
Bura, F. I., Pezzopane, R., Granados-Rodríguez, M., Rodríguez-Ortíz, L., Rufián‐Andújar, B., Martínez-López, A., Vazquez-Borrego, M. C., Romero‐Ruíz, A., & Arjona-Sánchez, Á. (2026) · Cirugía Española (English Edition) · doi:10.1016/j.cireng.2026.800303
Proteomics in the context of omics sciences: evaluation of tissue-specific responses in biomedical research
Gawor, A., & Bulska, E. (2026) · Pediatria i Medycyna Rodzinna · doi:10.15557/pimr.2025.0034
Experimental Evidence for Phosphorylation-Driven Allosteric Regulation of Alpha Synuclein FunctionPreprint
Dollar, A. N., & Webb, I. K. (2025) · bioRxiv · doi:10.1101/2025.02.20.639338
TopDIA: A Software Tool for Top-Down Data-Independent Acquisition Proteomics
Basharat, A. R., Xiong, X., Xu, T., Zang, Y., Sun, L., & Liu, X. (2024) · Journal of Proteome Research · doi:10.1021/acs.jproteome.4c00293 · Cited by 9
Comprehensive Characterization of Endogenous Phospholamban Proteoforms Enabled by Photocleavable Surfactant and Top-down Proteomics
Rogers, H. T., Roberts, D. S., Larson, E. J., Melby, J. A., Rossler, K. J., Carr, A. V., Brown, K. A., & Ge, Y. (2023) · bioRxiv · doi:10.1101/2023.04.12.536120
The Evolution of Proteomics from 2010 to 2020
Kamal, R. (2022) · International Journal of Innovative Research in Medical Science · doi:10.23958/ijirms/vol07-i03/1366
“difficulties, the top-down technique identifies as an essential complement and option to digestion-based approaches ([13]).”
Background
Quantitative metaproteomics of patient fecal microbiota identifies host and microbial proteins associated with ulcerative colitisPreprint
Thuy-Boun, P. S., Wang, A. Y., Crissien-Martinez, A., Xu, J. H., Chatterjee, S., Stupp, G. S., Su, A. I., Coyle, W., & Wolan, D. W. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.11.11.378836
Mode of action of a novel lymphocyte inhibitory factor of attaching and effacing Escherichia coli
Bease, A. (2020) · doi:10.7488/era/241
Techniques for Measuring Cellular Signal Transduction
Miller, J. V., Gao, W., Cromie, M. M., & Liu, Z. (2019) · Wiley eBooks · doi:10.1002/9781119060208.ch6
Proteômica top-down da bactéria produtora de aminoácidos Corynebacterium glutamicum
Melo, R. (2019) · doi:10.26512/2019.02.d.35356
“Adaptado de Catherman et al., 2014.”

Authors: Catherman, A. D., Skinner, O. S., & Kelleher, N. L.
Affiliations: Northwestern University (US)
Corresponding author: Kelleher, Neil L.
ORCID: Skinner, Owen S.
Kelleher, Neil L.
Venue: Biochemical and Biophysical Research Communications
Publisher: Elsevier BV
Published: 2014-03
Volume: 445
Issue: 4
Pages: 683-693
ISSN: 0006-291X (ISSN-L)
DOI: 10.1016/j.bbrc.2014.02.041
PMC: PMC4103433
OpenAlex: W2070948666
Cited by: 507
References: 143
Citations by year: 2026: 21 · 2025: 32 · 2024: 31 · 2023: 37 · 2022: 48 · 2021: 49 · 2020: 49 · 2019: 46 · 2018: 41 · 2017: 59 · 2016: 38 · 2015: 42 · 2014: 14
FWCI: 5.00
Type: journal article
Language: en
Open access: green
www.ncbi.nlm.nih.gov
Licence: www.elsevier.com/tdm/userlicense/1.0/ (tdm)
Locations: Biochemical and Biophysical Research Communications (publishedVersion)
PubMed (publishedVersion)
PubMed Central (acceptedVersion)
Funders: National Institute of General Medical Sciences (R01GM067193)
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: top-down proteomics, post-translational modification, protein characterization, protein separation, protein complex identification
MeSH terms: Amino Acid Sequence, Animals, Chromatography, Liquid, Electrophoresis, Equipment Design, Humans, Molecular Sequence Data, Proteins, Mass Spectrometry, Proteomics

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