Data‐independent acquisition‐based SWATH‐MS for quantitative proteomics: a tutorial

C Ludwig, L Gillet, G Rosenberger, S Amon… - Molecular systems …, 2018 - embopress.org
Many research questions in fields such as personalized medicine, drug screens or systems
biology depend on obtaining consistent and quantitatively accurate proteomics data from …

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 …

[HTML][HTML] New agents for the treatment of drug-resistant Mycobacterium tuberculosis

DT Hoagland, J Liu, RB Lee, RE Lee - Advanced drug delivery reviews, 2016 - Elsevier
Inadequate dosing and incomplete treatment regimens, coupled with the ability of the
tuberculosis bacilli to cause latent infections that are tolerant of currently used drugs, have …

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 …

[HTML][HTML] Human SRMAtlas: a resource of targeted assays to quantify the complete human proteome

U Kusebauch, DS Campbell, EW Deutsch, CS Chu… - Cell, 2016 - cell.com
The ability to reliably and reproducibly measure any protein of the human proteome in any
tissue or cell type would be transformative for understanding systems-level properties as …

Building high-quality assay libraries for targeted analysis of SWATH MS data

OT Schubert, LC Gillet, BC Collins, P Navarro… - Nature protocols, 2015 - nature.com
Targeted proteomics by selected/multiple reaction monitoring (S/MRM) or, on a larger scale,
by SWATH (sequential window acquisition of all theoretical spectra) MS (mass spectrometry) …

Statistical control of peptide and protein error rates in large-scale targeted data-independent acquisition analyses

G Rosenberger, I Bludau, U Schmitt, M Heusel… - Nature …, 2017 - nature.com
Liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) is the main
method for high-throughput identification and quantification of peptides and inferred …

Multiplexed peptide analysis using data-independent acquisition and Skyline

JD Egertson, B MacLean, R Johnson, Y Xuan… - Nature protocols, 2015 - nature.com
Here we describe the use of data-independent acquisition (DIA) on a Q-Exactive mass
spectrometer for the detection and quantification of peptides in complex mixtures using the …

Absolute proteome composition and dynamics during dormancy and resuscitation of Mycobacterium tuberculosis

OT Schubert, C Ludwig, M Kogadeeva… - Cell host & …, 2015 - cell.com
Mycobacterium tuberculosis remains a health concern due to its ability to enter a non-
replicative dormant state linked to drug resistance. Understanding transitions into and out of …