Top-down proteomics

DS Roberts, JA Loo, YO Tsybin, X Liu, S Wu… - Nature Reviews …, 2024‏ - nature.com
Proteoforms, which arise from post-translational modifications, genetic polymorphisms and
RNA splice variants, play a pivotal role as drivers in biology. Understanding proteoforms is …

Top-down proteomics and the challenges of true proteoform characterization

A Po, CE Eyers - Journal of proteome research, 2023‏ - ACS Publications
Top-down proteomics (TDP) aims to identify and profile intact protein forms (proteoforms)
extracted from biological samples. True proteoform characterization requires that both the …

The Blood Proteoform Atlas: A reference map of proteoforms in human hematopoietic cells

RD Melani, VR Gerbasi, LC Anderson, JW Sikora… - Science, 2022‏ - science.org
Human biology is tightly linked to proteins, yet most measurements do not precisely
determine alternatively spliced sequences or posttranslational modifications. Here, we …

The human proteoform project: defining the human proteome

LM Smith, JN Agar, J Chamot-Rooke, PO Danis… - Science …, 2021‏ - science.org
Proteins are the primary effectors of function in biology, and thus, complete knowledge of
their structure and properties is fundamental to deciphering function in basic and …

Overview and considerations in bottom-up proteomics

RM Miller, LM Smith - Analyst, 2023‏ - pubs.rsc.org
Proteins are the key biological actors within cells, driving many biological processes integral
to both healthy and diseased states. Understanding the depth of complexity represented …

Top-down mass spectrometry of native proteoforms and their complexes: a community study

T Habeck, KA Brown, B Des Soye, C Lantz, M Zhou… - Nature …, 2024‏ - nature.com
The combination of native electrospray ionization with top-down fragmentation in mass
spectrometry (MS) allows simultaneous determination of the stoichiometry of noncovalent …

Mass spectrometry-based top-down proteomics in nanomedicine: proteoform-specific measurement of protein corona

SA Sadeghi, AA Ashkarran, Q Wang, G Zhu… - ACS …, 2024‏ - ACS Publications
Conventional mass spectrometry (MS)-based bottom-up proteomics (BUP) analysis of the
protein corona [ie, an evolving layer of biomolecules, mostly proteins, formed on the surface …

O-Pair Search with MetaMorpheus for O-glycopeptide characterization

L Lu, NM Riley, MR Shortreed, CR Bertozzi, LM Smith - Nature Methods, 2020‏ - nature.com
Abstract We report O-Pair Search, an approach to identify O-glycopeptides and localize O-
glycosites. Using paired collision-and electron-based dissociation spectra, O-Pair Search …

Ion activation methods for peptides and proteins

LA Macias, IC Santos, JS Brodbelt - Analytical chemistry, 2019‏ - ACS Publications
Mass spectrometry is well-established as one of the primary methods used to characterize
peptides and proteins. New advances in instrumentation and innovative analytical workflows …

MASH explorer: a universal software environment for top-down proteomics

Z Wu, DS Roberts, JA Melby, K Wenger… - Journal of proteome …, 2020‏ - ACS Publications
Top-down mass spectrometry (MS)-based proteomics enable a comprehensive analysis of
proteoforms with molecular specificity to achieve a proteome-wide understanding of protein …