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 Skyline ecosystem: Informatics for quantitative mass spectrometry proteomics

LK Pino, BC Searle, JG Bollinger… - Mass spectrometry …, 2020 - Wiley Online Library
Skyline is a freely available, open‐source Windows client application for accelerating
targeted proteomics experimentation, with an emphasis on the proteomics and mass …

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 …

Selected reaction monitoring–based proteomics: workflows, potential, pitfalls and future directions

P Picotti, R Aebersold - Nature methods, 2012 - nature.com
Selected reaction monitoring (SRM) is a targeted mass spectrometry technique that is
emerging in the field of proteomics as a complement to untargeted shotgun methods. SRM is …

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 …

[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 …

MaxQuant enables high peptide identification rates, individualized ppb-range mass accuracies and proteome-wide protein quantification

J Cox, M Mann - Nature biotechnology, 2008 - nature.com
Efficient analysis of very large amounts of raw data for peptide identification and protein
quantification is a principal challenge in mass spectrometry (MS)-based proteomics. Here …

The quantitative proteome of a human cell line

M Beck, A Schmidt, J Malmstroem… - Molecular systems …, 2011 - embopress.org
The generation of mathematical models of biological processes, the simulation of these
processes under different conditions, and the comparison and integration of multiple data …

Using i RT, a normalized retention time for more targeted measurement of peptides

C Escher, L Reiter, B MacLean, R Ossola… - …, 2012 - Wiley Online Library
Multiple reaction monitoring (MRM) has recently become the method of choice for targeted
quantitative measurement of proteins using mass spectrometry. The method, however, is …

Widespread changes in protein synthesis induced by microRNAs

M Selbach, B Schwanhäusser, N Thierfelder, Z Fang… - nature, 2008 - nature.com
Animal microRNAs (miRNAs) regulate gene expression by inhibiting translation and/or by
inducing degradation of target messenger RNAs. It is unknown how much translational …