A critical review of bottom-up proteomics: the good, the bad, and the future of this field

EJ Dupree, M Jayathirtha, H Yorkey, M Mihasan… - Proteomes, 2020 - mdpi.com
Proteomics is the field of study that includes the analysis of proteins, from either a basic
science prospective or a clinical one. Proteins can be investigated for their abundance …

Quantitative proteomic analysis of histone modifications

H Huang, S Lin, BA Garcia, Y Zhao - Chemical reviews, 2015 - ACS Publications
Several mechanisms have been proposed for histone marks to exert their functions,
including altering the physical properties of nucleosomes by neutralization of charge via …

Universal and confident phosphorylation site localization using phosphoRS

T Taus, T Köcher, P Pichler, C Paschke… - Journal of proteome …, 2011 - ACS Publications
An algorithm for the assignment of phosphorylation sites in peptides is described. The
program uses tandem mass spectrometry data in conjunction with the respective peptide …

Advances in structure elucidation of small molecules using mass spectrometry

T Kind, O Fiehn - Bioanalytical reviews, 2010 - Springer
The structural elucidation of small molecules using mass spectrometry plays an important
role in modern life sciences and bioanalytical approaches. This review covers different soft …

Photodissociation mass spectrometry: new tools for characterization of biological molecules

JS Brodbelt - Chemical Society Reviews, 2014 - pubs.rsc.org
Photodissociation mass spectrometry combines the ability to activate and fragment ions
using photons with the sensitive detection of the resulting product ions by mass …

An integrated native mass spectrometry and top-down proteomics method that connects sequence to structure and function of macromolecular complexes

H Li, HH Nguyen, RR Ogorzalek Loo… - Nature …, 2018 - nature.com
Mass spectrometry (MS) has become a crucial technique for the analysis of protein
complexes. Native MS has traditionally examined protein subunit arrangements, while …

Interpreting the protein language using proteomics

ON Jensen - Nature reviews Molecular cell biology, 2006 - nature.com
Post-translational modifications define the functional and structural plasticity of proteins in
archaea, prokaryotes and eukaryotes. Multi-site protein modification modulates protein …

Preparation of proteins and peptides for mass spectrometry analysis in a bottom‐up proteomics workflow

RL Gundry, MY White, CI Murray… - Current protocols in …, 2010 - Wiley Online Library
This unit outlines the steps required to prepare a sample for MS analysis following protein
separation or enrichment by gel electrophoresis, liquid chromatography, and affinity capture …

Ion activation methods for peptides and proteins

JS Brodbelt - Analytical chemistry, 2016 - ACS Publications
The analysis of peptides and proteins as well as the grander scope of proteomics (large
scale study of proteins) has been advanced by the development of a versatile array of ion …

Protein complexes in the gas phase: technology for structural genomics and proteomics

JLP Benesch, BT Ruotolo, DA Simmons… - Chemical …, 2007 - ACS Publications
How does the development of mass spectrometry (MS) for the study of protein complexes,
intact in the gas phase, contribute to the twin fields of genomics and proteomics? Foremost …