Targeted proteomics on its way to discovery

The Parallel Reaction Monitoring-Parallel Accumulation–Serial Fragmentation (prm-PASEF) Approach for Multiplexed Absolute Quantitation of Proteins in Human Plasma

(2022) Alexander Brzhozovskiy et al.   ANALYTICAL CHEMISTRY

Rapid Targeted Quantitation of Protein Overexpression with Direct Infusion Shotgun Proteome Analysis (DISPA-PRM)

(2022) Edna A. Trujillo et al.   ANALYTICAL CHEMISTRY

High‐throughput, in‐depth and estimated absolution quantification of plasma proteome using data‐independent acquisition/ mass spectrometry (“HIAP‐DIA”)

(2021) Yue Zhou et al.   PROTEOMICS

Ultra-fast proteomics with Scanning SWATH

(2021) Christoph B. Messner et al.   NATURE BIOTECHNOLOGY

MaxDIA enables library-based and library-free data-independent acquisition proteomics

(2021) Pavel Sinitcyn et al.   NATURE BIOTECHNOLOGY

PRM-LIVE with Trapped Ion Mobility Spectrometry and Its Application in Selectivity Profiling of Kinase Inhibitors

(2021) He Zhu et al.   ANALYTICAL CHEMISTRY

A Compact Quadrupole-Orbitrap Mass Spectrometer with FAIMS Interface Improves Proteome Coverage in Short LC Gradients

(2020) Dorte B. Bekker-Jensen et al.   MOLECULAR & CELLULAR PROTEOMICS

Data‐Independent Acquisition Mass Spectrometry‐Based Proteomics and Software Tools: A Glimpse in 2020

(2020) Fangfei Zhang et al.   PROTEOMICS

Ultra-High-Throughput Clinical Proteomics Reveals Classifiers of COVID-19 Infection

(2020) Christoph B. Messner et al.   Cell Systems

Highly Multiplexed Targeted Proteomics Acquisition on a TIMS-QTOF

(2020) Antoine Lesur et al.   ANALYTICAL CHEMISTRY

diaPASEF: parallel accumulation–serial fragmentation combined with data-independent acquisition

(2020) Florian Meier et al.   NATURE METHODS

Analysis of 1508 plasma samples by capillary flow data-independent acquisition profiles proteomics of weight loss and maintenance

(2019) Roland Bruderer et al.   MOLECULAR & CELLULAR PROTEOMICS

Prosit: proteome-wide prediction of peptide tandem mass spectra by deep learning

(2019) Siegfried Gessulat et al.   NATURE METHODS

High-quality MS/MS spectrum prediction for data-dependent and data-independent acquisition data analysis

(2019) Shivani Tiwary et al.   NATURE METHODS

DIA-NN: neural networks and interference correction enable deep proteome coverage in high throughput

(2019) Vadim Demichev et al.   NATURE METHODS

High throughput and accurate serum proteome profiling by integrated sample preparation technology and single-run data independent mass spectrometry analysis

(2018) Lin Lin et al.   Journal of Proteomics

BoxCar acquisition method enables single-shot proteomics at a depth of 10,000 proteins in 100 minutes

(2018) Florian Meier et al.   NATURE METHODS

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

(2018) Christina Ludwig et al.   Molecular Systems Biology

Plasma Proteome Profiling Reveals Dynamics of Inflammatory and Lipid Homeostasis Markers after Roux-En-Y Gastric Bypass Surgery

(2018) Nicolai J. Wewer Albrechtsen et al.   Cell Systems

Scanning Quadrupole Data-Independent Acquisition, Part A: Qualitative and Quantitative Characterization

(2017) M. Arthur Moseley et al.   JOURNAL OF PROTEOME RESEARCH

PECAN: library-free peptide detection for data-independent acquisition tandem mass spectrometry data

(2017) Ying S Ting et al.   NATURE METHODS

Mass-spectrometric exploration of proteome structure and function

(2016) Ruedi Aebersold et al.   NATURE

Application of wide selected-ion monitoring data-independent acquisition to identify tomato fruit proteins regulated by the CUTIN DEFICIENT2 transcription factor

(2016) Laetitia B. B. Martin et al.   PROTEOMICS

Advances in high-resolution quantitative proteomics: implications for clinical applications

(2015) Sebastien Gallien et al.   Expert Review of Proteomics

The Use of Variable Q1 Isolation Windows Improves Selectivity in LC–SWATH–MS Acquisition

(2015) Ying Zhang et al.   JOURNAL OF PROTEOME RESEARCH

Detection and quantification of proteins in clinical samples using high resolution mass spectrometry

(2015) Sebastien Gallien et al.   METHODS

Extending the Limits of Quantitative Proteome Profiling with Data-Independent Acquisition and Application to Acetaminophen-Treated Three-Dimensional Liver Microtissues

(2015) Roland Bruderer et al.   MOLECULAR & CELLULAR PROTEOMICS

Quantitative variability of 342 plasma proteins in a human twin population

(2015) Y. Liu et al.   Molecular Systems Biology

DIA-Umpire: comprehensive computational framework for data-independent acquisition proteomics

(2015) Chih-Chiang Tsou et al.   NATURE METHODS

Multiplexed peptide analysis using data-independent acquisition and Skyline

(2015) Jarrett D Egertson et al.   Nature Protocols

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

(2015) Tatjana Sajic et al.   Proteomics Clinical Applications

Hybrid Data Acquisition and Processing Strategies with Increased Throughput and Selectivity: pSMART Analysis for Global Qualitative and Quantitative Analysis

(2014) Amol Prakash et al.   JOURNAL OF PROTEOME RESEARCH

Simplified and Efficient Quantification of Low-abundance Proteins at Very High Multiplex via Targeted Mass Spectrometry

(2014) Michael W. Burgess et al.   MOLECULAR & CELLULAR PROTEOMICS

OpenSWATH enables automated, targeted analysis of data-independent acquisition MS data

(2014) Hannes L Röst et al.   NATURE BIOTECHNOLOGY

Advances in multiplexed MRM-based protein biomarker quantitation toward clinical utility

(2013) Andrew J. Percy et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

Recent advances in mass spectrometry: data independent analysis and hyper reaction monitoring

(2013) Kai Pong Law et al.   Expert Review of Proteomics

Selectivity of LC-MS/MS analysis: Implication for proteomics experiments

(2012) Sebastien Gallien et al.   Journal of Proteomics

Targeted Data Extraction of the MS/MS Spectra Generated by Data-independent Acquisition: A New Concept for Consistent and Accurate Proteome Analysis

(2012) Ludovic C. Gillet et al.   MOLECULAR & CELLULAR PROTEOMICS

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

(2012) Claudia Escher et al.   PROTEOMICS

More than 100,000 Detectable Peptide Species Elute in Single Shotgun Proteomics Runs but the Majority is Inaccessible to Data-Dependent LC−MS/MS

(2011) Annette Michalski et al.   JOURNAL OF PROTEOME RESEARCH

XDIA: improving on the label-free data-independent analysis

(2010) Paulo C. Carvalho et al.   BIOINFORMATICS

Proteomics on an Orbitrap Benchtop Mass Spectrometer Using All-ion Fragmentation

(2010) Tamar Geiger et al.   MOLECULAR & CELLULAR PROTEOMICS

Precursor Acquisition Independent From Ion Count: How to Dive Deeper into the Proteomics Ocean

(2009) Alexandre Panchaud et al.   ANALYTICAL CHEMISTRY

Selected reaction monitoring for quantitative proteomics: a tutorial

(2008) Vinzenz Lange et al.   Molecular Systems Biology