On the dependency of cellular protein levels on mRNA abundance

Y Liu, A Beyer, R Aebersold - Cell, 2016 - cell.com
The question of how genomic information is expressed to determine phenotypes is of central
importance for basic and translational life science research and has been studied by …

A review on mass spectrometry-based quantitative proteomics: Targeted and data independent acquisition

V Vidova, Z Spacil - Analytica chimica acta, 2017 - Elsevier
Mass spectrometry (MS) based proteomics have achieved a near-complete proteome
coverage in humans and in several other organisms, producing a wealth of information …

Extending the limits of quantitative proteome profiling with data-independent acquisition and application to acetaminophen-treated three-dimensional liver …

R Bruderer, OM Bernhardt, T Gandhi… - Molecular & Cellular …, 2015 - ASBMB
The data-independent acquisition (DIA) approach has recently been introduced as a novel
mass spectrometric method that promises to combine the high content aspect of shotgun …

A novel LC system embeds analytes in pre-formed gradients for rapid, ultra-robust proteomics

N Bache, PE Geyer, DB Bekker-Jensen… - Molecular & Cellular …, 2018 - ASBMB
To further integrate mass spectrometry (MS)-based proteomics into biomedical research and
especially into clinical settings, high throughput and robustness are essential requirements …

A repository of assays to quantify 10,000 human proteins by SWATH-MS

G Rosenberger, CC Koh, T Guo, HL Röst, P Kouvonen… - Scientific data, 2014 - nature.com
Mass spectrometry is the method of choice for deep and reliable exploration of the (human)
proteome. Targeted mass spectrometry reliably detects and quantifies pre-determined sets …

Quantitative variability of 342 plasma proteins in a human twin population

Y Liu, A Buil, BC Collins, LCJ Gillet… - Molecular systems …, 2015 - embopress.org
The degree and the origins of quantitative variability of most human plasma proteins are
largely unknown. Because the twin study design provides a natural opportunity to estimate …

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 …

SWATH‐MS as a tool for biomarker discovery: From basic research to clinical applications

SI Anjo, C Santa, B Manadas - Proteomics, 2017 - Wiley Online Library
In the era of quantitative proteomics, where mass spectrometry plays a pivotal role, in
particular associated with the use of data‐independent acquisition, it is time to perform an …

Using data‐independent, high‐resolution mass spectrometry in protein biomarker research: perspectives and clinical applications

T Sajic, Y Liu, R Aebersold - PROTEOMICS–Clinical …, 2015 - Wiley Online Library
In medicine, there is an urgent need for protein biomarkers in a range of applications that
includes diagnostics, disease stratification, and therapeutic decisions. One of the main …