Workflows for automated downstream data analysis and visualization in large‐scale computational mass spectrometry
journal
February 2015
New algorithms for processing and peak detection in liquid chromatography/mass spectrometry data
journal
January 2002
Comparative evaluation of extraction methods for simultaneous mass-spectrometric analysis of complex lipids and primary metabolites from human blood plasma
journal
August 2014
Ion Mobility Spectrometry: Fundamental Concepts, Instrumentation, Applications, and the Road Ahead
journal
September 2019
Aligning of single and multiple wavelength chromatographic profiles for chemometric data analysis using correlation optimised warping
journal
May 1998
Data processing for mass spectrometry-based metabolomics
journal
July 2007
SPE-IMS-MS: An automated platform for sub-sixty second surveillance of endogenous metabolites and xenobiotics in biofluids
journal
December 2016
XCMS: Processing Mass Spectrometry Data for Metabolite Profiling Using Nonlinear Peak Alignment, Matching, and Identification
journal
February 2006
MET-IDEA: Data Extraction Tool for Mass Spectrometry-Based Metabolomics
journal
July 2006
Chromatographic Alignment of ESI-LC-MS Proteomics Data Sets by Ordered Bijective Interpolated Warping
journal
September 2006
Metabolomic Analysis and Visualization Engine for LC−MS Data
journal
December 2010
Metabolite Profiling of a NIST Standard Reference Material for Human Plasma (SRM 1950): GC-MS, LC-MS, NMR, and Clinical Laboratory Analyses, Libraries, and Web-Based Resources
journal
November 2013
Ion Mobility Derived Collision Cross Sections to Support Metabolomics Applications
journal
March 2014
Ion Mobility-Mass Spectrometry: Time-Dispersive Instrumentation
journal
January 2015
XCMS 2 : Processing Tandem Mass Spectrometry Data for Metabolite Identification and Structural Characterization
journal
July 2008
Correlation-Based Deconvolution (CorrDec) To Generate High-Quality MS2 Spectra from Data-Independent Acquisition in Multisample Studies
journal
July 2020
A Practical Guide to Metabolomics Software Development
journal
January 2021
Ultra-High Resolution Ion Mobility Separations Utilizing Traveling Waves in a 13 m Serpentine Path Length Structures for Lossless Ion Manipulations Module
journal
August 2016
Visualization, Quantification, and Alignment of Spectral Drift in Population Scale Untargeted Metabolomics Data
journal
January 2017
Mass Spectral Feature List Optimizer (MS-FLO): A Tool To Minimize False Positive Peak Reports in Untargeted Liquid Chromatography–Mass Spectroscopy (LC-MS) Data Processing
journal
March 2017
An Interlaboratory Evaluation of Drift Tube Ion Mobility–Mass Spectrometry Collision Cross Section Measurements
journal
August 2017
Increasing Compound Identification Rates in Untargeted Lipidomics Research with Liquid Chromatography Drift Time–Ion Mobility Mass Spectrometry
journal
August 2018
ADAP-GC 4.0: Application of Clustering-Assisted Multivariate Curve Resolution to Spectral Deconvolution of Gas Chromatography–Mass Spectrometry Metabolomics Data
journal
June 2019
DecoMetDIA: Deconvolution of Multiplexed MS/MS Spectra for Metabolite Identification in SWATH-MS-Based Untargeted Metabolomics
journal
August 2019
Mass Spectrometry Adduct Calculator
journal
November 2021
Evaluation of In Silico Multifeature Libraries for Providing Evidence for the Presence of Small Molecules in Synthetic Blinded Samples
journal
June 2019
Wavelet-Based Peak Detection and a New Charge Inference Procedure for MS/MS Implemented in ProteoWizard’s msConvert
journal
December 2014
Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking
journal
August 2016
The power of ion mobility-mass spectrometry for structural characterization and the study of conformational dynamics
journal
March 2014
OpenMS: a flexible open-source software platform for mass spectrometry data analysis
journal
August 2016
Array programming with NumPy
journal
September 2020
SciPy 1.0: fundamental algorithms for scientific computing in Python
journal
February 2020
Combining ultra-high resolution ion mobility spectrometry with cryogenic IR spectroscopy for the study of biomolecular ions
journal
January 2019
Efficient Analysis of Mass Spectrometry Data Using the Isotope Wavelet
Hussong, Rene; Tholey, Andreas; Hildebrandt, Andreas
COMPLIFE 2007: The Third International Symposium on Computational Life Science, AIP Conference Proceedings
https://doi.org/10.1063/1.2793396
conference
January 2007
mzML—a Community Standard for Mass Spectrometry Data
journal
August 2010
DIAlignR Provides Precise Retention Time Alignment Across Distant Runs in DIA and Targeted Proteomics
journal
April 2019
AutoCCS: automated collision cross-section calculation software for ion mobility spectrometry–mass spectrometry
journal
June 2021
Improved peak detection in mass spectrum by incorporating continuous wavelet transform-based pattern matching
journal
July 2006
VIPER: an advanced software package to support high-throughput LC-MS peptide identification
journal
June 2007
ProteoWizard: open source software for rapid proteomics tools development
journal
July 2008
A dynamic wavelet-based algorithm for pre-processing tandem mass spectrometry data
journal
July 2010
Snakemake--a scalable bioinformatics workflow engine
journal
August 2012
eMZed: an open source framework in Python for rapid and interactive development of LC/MS data analysis workflows
journal
February 2013
LC-IMS-MS Feature Finder: detecting multidimensional liquid chromatography, ion mobility and mass spectrometry features in complex datasets
journal
September 2013
LIQUID: an-open source software for identifying lipids in LC-MS/MS-based lipidomics data
journal
January 2017
MetaboAnalyst 4.0: towards more transparent and integrative metabolomics analysis
journal
May 2018
MetaboLights: a resource evolving in response to the needs of its scientific community
journal
November 2019
MZmine 2: Modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data
journal
July 2010
Highly sensitive feature detection for high resolution LC/MS
journal
November 2008
Lipid extraction by methyl- tert -butyl ether for high-throughput lipidomics
journal
February 2008
A Case Report of Switching from Specific Vendor-Based to R-Based Pipelines for Untargeted LC-MS Metabolomics
journal
January 2020
Integrating ion mobility spectrometry into mass spectrometry-based exposome measurements: what can it add and how far can it go?
journal
January 2017