Selected reaction monitoring–based proteomics: workflows, potential, pitfalls and future directions

P Picotti, R Aebersold - Nature methods, 2012 - nature.com
Selected reaction monitoring (SRM) is a targeted mass spectrometry technique that is
emerging in the field of proteomics as a complement to untargeted shotgun methods. SRM is …

Chemical glycoproteomics

KK Palaniappan, CR Bertozzi - Chemical reviews, 2016 - ACS Publications
Chemical tools have accelerated progress in glycoscience, reducing experimental barriers
to studying protein glycosylation, the most widespread and complex form of posttranslational …

Clinical potential of mass spectrometry-based proteogenomics

B Zhang, JR Whiteaker, AN Hoofnagle… - Nature Reviews …, 2019 - nature.com
Cancer genomics research aims to advance personalized oncology by finding and targeting
specific genetic alterations associated with cancers. In genome-driven oncology, treatments …

On the development of plasma protein biomarkers

S Surinova, R Schiess, R Hüttenhain… - Journal of proteome …, 2011 - ACS Publications
The development of plasma biomarkers has proven to be more challenging than initially
anticipated. Many studies have reported lists of candidate proteins rather than validated …

Redox proteomics: chemical principles, methodological approaches and biological/biomedical promises

A Bachi, I Dalle-Donne, A Scaloni - Chemical reviews, 2013 - ACS Publications
Inevitable byproducts of aerobic metabolism are free radicals and other highly reactive
oxidants and nitrosants that are continuously formed within cells. Most cells generally …

Reproducible quantification of cancer-associated proteins in body fluids using targeted proteomics

R Hüttenhain, M Soste, N Selevsek, H Röst… - Science translational …, 2012 - science.org
The rigorous testing of hypotheses on suitable sample cohorts is a major limitation in
translational research. This is particularly the case for the validation of protein biomarkers; …

Effect of collision energy optimization on the measurement of peptides by selected reaction monitoring (SRM) mass spectrometry

B MacLean, DM Tomazela, SE Abbatiello… - Analytical …, 2010 - ACS Publications
Proteomics experiments based on Selected Reaction Monitoring (SRM, also referred to as
Multiple Reaction Monitoring or MRM) are being used to target large numbers of protein …

Quantitative measurements of N‐linked glycoproteins in human plasma by SWATH‐MS

Y Liu, R Hüttenhain, S Surinova, LCJ Gillet… - …, 2013 - Wiley Online Library
SWATH‐MS is a data‐independent acquisition method that generates, in a single
measurement, a complete recording of the fragment ion spectra of all the analytes in a …

SWATH enables precise label‐free quantification on proteome scale

Q Huang, LU Yang, JI Luo, L Guo, Z Wang, X Yang… - …, 2015 - Wiley Online Library
MS‐based proteomics has emerged as a powerful tool in biological studies. The shotgun
proteomics strategy, in which proteolytic peptides are analyzed in data‐dependent mode …

Analysis of high accuracy, quantitative proteomics data in the MaxQB database

C Schaab, T Geiger, G Stoehr, J Cox… - Molecular & Cellular …, 2012 - ASBMB
MS-based proteomics generates rapidly increasing amounts of precise and quantitative
information. Analysis of individual proteomic experiments has made great strides, but the …