Advancing untargeted metabolomics using data-independent acquisition mass spectrometry technology

Metabolomic spectral libraries for data-independent SWATH liquid chromatography mass spectrometry acquisition

(2018) Tobias Bruderer et al.   ANALYTICAL AND BIOANALYTICAL CHEMISTRY

SWATHtoMRM: Development of High-Coverage Targeted Metabolomics Method Using SWATH Technology for Biomarker Discovery

(2018) Haihong Zha et al.   ANALYTICAL CHEMISTRY

Advancing the large-scale CCS database for metabolomics and lipidomics at the machine-learning era

(2018) Zhiwei Zhou et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

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

(2018) Christina Ludwig et al.   Molecular Systems Biology

SWATH data independent acquisition mass spectrometry for metabolomics

(2018) Ron Bonner et al.   TRAC-TRENDS IN ANALYTICAL CHEMISTRY

The use of LC predicted retention times to extend metabolites identification with SWATH data acquisition

(2017) Tobias Bruderer et al.   JOURNAL OF CHROMATOGRAPHY B-ANALYTICAL TECHNOLOGIES IN THE BIOMEDICAL AND LIFE SCIENCES

MetDIA: Targeted Metabolite Extraction of Multiplexed MS/MS Spectra Generated by Data-Independent Acquisition

(2016) Hao Li et al.   ANALYTICAL CHEMISTRY

Development and Evaluation of a Parallel Reaction Monitoring Strategy for Large-Scale Targeted Metabolomics Quantification

(2016) Juntuo Zhou et al.   ANALYTICAL CHEMISTRY

Integrating MS1 and MS2 Scans in High-Resolution Parallel Reaction Monitoring Assays for Targeted Metabolite Quantification and Dynamic 13C-Labeling Metabolism Analysis

(2016) Zhucui Li et al.   ANALYTICAL CHEMISTRY

ADAP-GC 3.0: Improved Peak Detection and Deconvolution of Co-eluting Metabolites from GC/TOF-MS Data for Metabolomics Studies

(2016) Yan Ni et al.   ANALYTICAL CHEMISTRY

Untargeted Metabolomics Strategies—Challenges and Emerging Directions

(2016) Alexandra C. Schrimpe-Rutledge et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

OpenMS: a flexible open-source software platform for mass spectrometry data analysis

(2016) Hannes L Röst et al.   NATURE METHODS

Metabolomics: beyond biomarkers and towards mechanisms

(2016) Caroline H. Johnson et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Toward Merging Untargeted and Targeted Methods in Mass Spectrometry-Based Metabolomics and Lipidomics

(2015) Tomas Cajka et al.   ANALYTICAL CHEMISTRY

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

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

An integrated targeted metabolomic platform for high-throughput metabolite profiling and automated data processing

(2015) Yuping Cai et al.   Metabolomics

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

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

MS-DIAL: data-independent MS/MS deconvolution for comprehensive metabolome analysis

(2015) Hiroshi Tsugawa et al.   NATURE METHODS

RAMClust: A Novel Feature Clustering Method Enables Spectral-Matching-Based Annotation for Metabolomics Data

(2014) C. D. Broeckling et al.   ANALYTICAL CHEMISTRY

Integrated Quantification and Identification of Aldehydes and Ketones in Biological Samples

(2014) David Siegel et al.   ANALYTICAL CHEMISTRY

Liquid Chromatography, in Combination with a Quadrupole Time-of-Flight Instrument (LC QTOF), with Sequential Window Acquisition of All Theoretical Fragment-Ion Spectra (SWATH) Acquisition: Systematic Studies on Its Use for Screenings in Clinical and Forensic Toxicology and Comparison with Information-Dependent Acquisition (IDA)

(2014) Andreas T. Roemmelt et al.   ANALYTICAL CHEMISTRY

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

(2014) Hannes L Röst et al.   NATURE BIOTECHNOLOGY

Comparison of Information-Dependent Acquisition, SWATH, and MSAll Techniques in Metabolite Identification Study Employing Ultrahigh-Performance Liquid Chromatography–Quadrupole Time-of-Flight Mass Spectrometry

(2013) Xiaochun Zhu et al.   ANALYTICAL CHEMISTRY

Multiplexed MS/MS for improved data-independent acquisition

(2013) Jarrett D Egertson et al.   NATURE METHODS

Liquid chromatography quadrupole time-of-flight mass spectrometry characterization of metabolites guided by the METLIN database

(2013) Zheng-Jiang Zhu et al.   Nature Protocols

Assigning precursor–product ion relationships in indiscriminant MS/MS data from non-targeted metabolite profiling studies

(2012) Corey D. Broeckling et al.   Metabolomics

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

Metabolomics: the apogee of the omics trilogy

(2012) Gary J. Patti et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

High-resolution mass spectrometry for integrated qualitative and quantitative analysis of pharmaceuticals in biological matrices

(2011) Gérard Hopfgartner et al.   ANALYTICAL AND BIOANALYTICAL CHEMISTRY

Skyline: an open source document editor for creating and analyzing targeted proteomics experiments

(2010) Brendan MacLean et al.   BIOINFORMATICS

MZmine 2: Modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data

(2010) Tomáš Pluskal et al.   BMC BIOINFORMATICS

MassBank: a public repository for sharing mass spectral data for life sciences

(2010) Hisayuki Horai et al.   JOURNAL OF MASS SPECTROMETRY

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

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

Global metabolic profiling procedures for urine using UPLC–MS

(2010) Elizabeth J Want et al.   Nature Protocols

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

(2009) Alexandre Panchaud et al.   ANALYTICAL CHEMISTRY