Quantitative mass spectrometry-based proteomics: an overview

S Rozanova, K Barkovits, M Nikolov, C Schmidt… - Quantitative methods in …, 2021 - Springer
In recent decades, mass spectrometry has moved more than ever before into the front line of
protein-centered research. After being established at the qualitative level, the more …

Revisiting biomarker discovery by plasma proteomics

PE Geyer, LM Holdt, D Teupser… - Molecular systems biology, 2017 - embopress.org
Clinical analysis of blood is the most widespread diagnostic procedure in medicine, and
blood biomarkers are used to categorize patients and to support treatment decisions …

MatrisomeDB 2.0: 2023 updates to the ECM-protein knowledge database

X Shao, CD Gomez, N Kapoor… - Nucleic acids …, 2023 - academic.oup.com
The extracellular matrix (ECM) is a complex assembly of proteins that constitutes the scaffold
organizing cells, tissues, and organs. Over the past decade, mass-spectrometry-based …

A multicenter study benchmarks software tools for label-free proteome quantification

P Navarro, J Kuharev, LC Gillet, OM Bernhardt… - Nature …, 2016 - nature.com
Consistent and accurate quantification of proteins by mass spectrometry (MS)-based
proteomics depends on the performance of instruments, acquisition methods and data …

Advances in targeted proteomics and applications to biomedical research

T Shi, E Song, S Nie, KD Rodland, T Liu, WJ Qian… - …, 2016 - Wiley Online Library
Targeted proteomics technique has emerged as a powerful protein quantification tool in
systems biology, biomedical research, and increasing for clinical applications. The most …

Analysis of major histocompatibility complex (MHC) immunopeptidomes using mass spectrometry

E Caron, DJ Kowalewski, CC Koh, T Sturm… - Molecular & Cellular …, 2015 - ASBMB
The myriad of peptides presented at the cell surface by class I and class II major
histocompatibility complex (MHC) molecules are referred to as the immunopeptidome and …

Reproducibility, specificity and accuracy of relative quantification using spectral library-based data-independent acquisition

K Barkovits, S Pacharra, K Pfeiffer, S Steinbach… - Molecular & Cellular …, 2020 - ASBMB
Currently data-dependent acquisition (DDA) is the method of choice for mass spectrometry-
based proteomics discovery experiments, but data-independent acquisition (DIA) is steadily …

A relative quantitative positive/negative ion switching method for untargeted lipidomics via high resolution LC-MS/MS from any biological source

SB Breitkopf, SJH Ricoult, M Yuan, Y Xu, DA Peake… - Metabolomics, 2017 - Springer
Introduction Advances in high-resolution mass spectrometry have created renewed interest
for studying global lipid biochemistry in disease and biological systems. Objectives Here, we …

Clinical applications of quantitative proteomics using targeted and untargeted data-independent acquisition techniques

JG Meyer, B Schilling - Expert review of proteomics, 2017 - Taylor & Francis
Introduction: While selected/multiple-reaction monitoring (SRM or MRM) is considered the
gold standard for quantitative protein measurement, emerging data-independent acquisition …

Digital detection of proteins

DC Duffy - Lab on a Chip, 2023 - pubs.rsc.org
This paper reviews methods for detecting proteins based on molecular digitization, ie, the
isolation and detection of single protein molecules or singulated ensembles of protein …