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 …

The basics of mass spectrometry in the twenty-first century

GL Glish, RW Vachet - Nature reviews drug discovery, 2003 - nature.com
Enormous advances in our understanding of the chemistry underlying life processes have
identified new targets for therapeutic agents. The discovery of effective therapeutics to …

Mass spectrometry in proteomics

R Aebersold, DR Goodlett - Chemical reviews, 2001 - ACS Publications
Proteomics can be viewed as an experimental approach to explain the information
contained in genomic sequences in terms of the structure, function, and control of biological …

Ion activation methods for peptides and proteins

JS Brodbelt - Analytical chemistry, 2016 - ACS Publications
The analysis of peptides and proteins as well as the grander scope of proteomics (large
scale study of proteins) has been advanced by the development of a versatile array of ion …

The detection, correlation, and comparison of peptide precursor and product ions from data independent LC‐MS with data dependant LC‐MS/MS

SJ Geromanos, JPC Vissers, JC Silva… - …, 2009 - Wiley Online Library
The detection, correlation, and comparison of peptide and product ions from a data
independent LC‐MS acquisition strategy with data dependent LC‐MS/MS is described. The …

Multiplexed and data‐independent tandem mass spectrometry for global proteome profiling

JD Chapman, DR Goodlett… - Mass spectrometry …, 2014 - Wiley Online Library
One of the most important early developments in the field of proteomics was the advent of
automated data acquisition routines that allowed high‐throughput unattended data …

Proteomics by FTICR mass spectrometry: top down and bottom up

B Bogdanov, RD Smith - Mass spectrometry reviews, 2005 - Wiley Online Library
This review provides a broad overview of recent Fourier transform ion cyclotron resonance
(FTICR) applications and technological developments relevant to the field of proteomics …

Extensive and accurate benchmarking of DIA acquisition methods and software tools using a complex proteomic standard

C Gotti, F Roux-Dalvai… - Journal of proteome …, 2021 - ACS Publications
Over the past decade, the data-independent acquisition mode has gained popularity for
broad coverage of complex proteomes by LC-MS/MS and quantification of low-abundance …

Precursor acquisition independent from ion count: how to dive deeper into the proteomics ocean

A Panchaud, A Scherl, SA Shaffer… - Analytical …, 2009 - ACS Publications
Data-dependent precursor ion selection is widely used in shotgun proteomics to profile the
protein components of complex samples. Although very popular, this bottom-up method …

High-efficiency nanoscale liquid chromatography coupled on-line with mass spectrometry using nanoelectrospray ionization for proteomics

Y Shen, R Zhao, SJ Berger, GA Anderson… - Analytical …, 2002 - ACS Publications
We describe high-efficiency (peak capacities of∼ 103) nanoscale (using column inner
diameters down to 15 μ m) liquid chromatography (nanoLC)/low flow rate electrospray …