Mass spectrometry applied to bottom-up proteomics: entering the high-throughput era for hypothesis testing

LC Gillet, A Leitner, R Aebersold - Annual review of analytical …, 2016 - annualreviews.org
Proteins constitute a key class of molecular components that perform essential biochemical
reactions in living cells. Whether the aim is to extensively characterize a given protein or to …

Quantitative mass spectrometry in proteomics: critical review update from 2007 to the present

M Bantscheff, S Lemeer, MM Savitski… - Analytical and bioanalytical …, 2012 - Springer
Mass-spectrometry-based proteomics is continuing to make major contributions to the
discovery of fundamental biological processes and, more recently, has also developed into …

IonQuant enables accurate and sensitive label-free quantification with FDR-controlled match-between-runs

F Yu, SE Haynes, AI Nesvizhskii - Molecular & Cellular Proteomics, 2021 - ASBMB
Missing values weaken the power of label-free quantitative proteomic experiments to
uncover true quantitative differences between biological samples or experimental …

Drift time-specific collision energies enable deep-coverage data-independent acquisition proteomics

U Distler, J Kuharev, P Navarro, Y Levin, H Schild… - Nature …, 2014 - nature.com
We present a data-independent acquisition mass spectrometry method, ultradefinition (UD)
MSE. This approach utilizes ion mobility drift time-specific collision-energy profiles to …

MPLEx: a robust and universal protocol for single-sample integrative proteomic, metabolomic, and lipidomic analyses

ES Nakayasu, CD Nicora, AC Sims… - …, 2016 - Am Soc Microbiol
Integrative multi-omics analyses can empower more effective investigation and complete
understanding of complex biological systems. Despite recent advances in a range of omics …

Sources of technical variability in quantitative LC–MS proteomics: human brain tissue sample analysis

PD Piehowski, VA Petyuk, DJ Orton, F Xie… - Journal of proteome …, 2013 - ACS Publications
To design a robust quantitative proteomics study, an understanding of both the inherent
heterogeneity of the biological samples being studied as well as the technical variability of …

Extending the depth of human plasma proteome coverage using simple fractionation techniques

G Kaur, A Poljak, SA Ali, L Zhong… - Journal of proteome …, 2021 - ACS Publications
Human plasma is one of the most widely used tissues in clinical analysis, and plasma-based
biomarkers are used for monitoring patient health status and/or response to medical …

New mass spectrometry technologies contributing towards comprehensive and high throughput omics analyses of single cells

SP Couvillion, Y Zhu, G Nagy, JN Adkins, C Ansong… - Analyst, 2019 - pubs.rsc.org
Mass-spectrometry based omics technologies–namely proteomics, metabolomics and
lipidomics–have enabled the molecular level systems biology investigation of organisms in …

Improving Qualitative and Quantitative Performance for MSE-based Label-free Proteomics

NJ Bond, PV Shliaha, KS Lilley… - Journal of proteome …, 2013 - ACS Publications
Label-free quantitation by data independent methods (for instance MSE) is growing in
popularity due to the high technical reproducibility of mass spectrometry analysis. The recent …

Mycobacterium tuberculosis Ser/Thr Protein Kinase B Mediates an Oxygen-Dependent Replication Switch

C Ortega, R Liao, LN Anderson, T Rustad… - PLoS …, 2014 - journals.plos.org
The majority of Mycobacterium tuberculosis (Mtb) infections are clinically latent,
characterized by drug tolerance and little or no bacterial replication. Low oxygen tension is a …