Comparative Analyses of Data Independent Acquisition Mass Spectrometric Approaches: DIA, WiSIM-DIA, and Untargeted DIA

Optimization of Acquisition and Data-Processing Parameters for Improved Proteomic Quantification by Sequential Window Acquisition of All Theoretical Fragment Ion Mass Spectrometry

(2017) Shanshan Li et al.   JOURNAL OF PROTEOME RESEARCH

SWATH-ID: An instrument method which combines identification and quantification in a single analysis

(2017) Yang Kang et al.   PROTEOMICS

An Optimized Shotgun Strategy for the Rapid Generation of Comprehensive Human Proteomes

(2017) Dorte B. Bekker-Jensen et al.   Cell Systems

Profiling the human hippocampal proteome at all pathologic stages of Alzheimer's disease

(2016) David C. Hondius et al.   Alzheimers & Dementia

Untargeted, spectral library-free analysis of data-independent acquisition proteomics data generated using Orbitrap mass spectrometers

(2016) Chih-Chiang Tsou et al.   PROTEOMICS

Group 1 metabotropic glutamate receptors 1 and 5 form a protein complex in mouse hippocampus and cortex

(2016) Nikhil J. Pandya et al.   PROTEOMICS

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

High-precision iRT prediction in the targeted analysis of data-independent acquisition and its impact on identification and quantitation

(2016) Roland Bruderer et al.   PROTEOMICS

Dynamics of the mouse brain cortical synaptic proteome during postnatal brain development

(2016) Miguel A. Gonzalez-Lozano et al.   Scientific Reports

Opening a SWATH Window on Posttranslational Modifications: Automated Pursuit of Modified Peptides

(2015) Andrew Keller et al.   MOLECULAR & CELLULAR PROTEOMICS

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

Group-DIA: analyzing multiple data-independent acquisition mass spectrometry data files

(2015) Yuanyue Li et al.   NATURE METHODS

MSPLIT-DIA: sensitive peptide identification for data-independent acquisition

(2015) Jian Wang et al.   NATURE METHODS

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

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

2016 update of the PRIDE database and its related tools

(2015) Juan Antonio Vizcaíno et al.   NUCLEIC ACIDS RESEARCH

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

(2014) Hannes L Röst et al.   NATURE BIOTECHNOLOGY

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

Identification of phosphorylated human peptides by accurate mass measurement alone

(2011) Yuan Mao et al.   INTERNATIONAL JOURNAL OF MASS SPECTROMETRY

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

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

(2008) Jürgen Cox et al.   NATURE BIOTECHNOLOGY