In Silico Optimization of Mass Spectrometry Fragmentation Strategies in Metabolomics

Rapid Prediction of Electron–Ionization Mass Spectrometry Using Neural Networks

(2019) Jennifer N. Wei et al.   ACS Central Science

SIRIUS 4: a rapid tool for turning tandem mass spectra into metabolite structure information

(2019) Kai Dührkop et al.   NATURE METHODS

MolNetEnhancer: Enhanced Molecular Networks by Integrating Metabolome Mining and Annotation Tools

(2019) Madeleine Ernst et al.   Metabolites

Comprehensive Tandem-Mass-Spectrometry Coverage of Complex Samples Enabled by Data-Set-Dependent Acquisition

(2018) Corey D. Broeckling et al.   ANALYTICAL CHEMISTRY

pymzML v2.0: introducing a highly compressed and seekable gzip format

(2018) M Kösters et al.   BIOINFORMATICS

MaSS-Simulator: A Highly Configurable Simulator for Generating MS/MS Datasets for Benchmarking of Proteomics Algorithms

(2018) Muaaz Gul Awan et al.   PROTEOMICS

psims - A declarative writer for mzML and mzIdentML for Python

(2018) Joshua A. Klein et al.   MOLECULAR & CELLULAR PROTEOMICS

HMDB 4.0: the human metabolome database for 2018

(2017) David S Wishart et al.   NUCLEIC ACIDS RESEARCH

Nested data independent MS/MS acquisition

(2016) Anton Kaufmann et al.   ANALYTICAL AND BIOANALYTICAL CHEMISTRY

Topic modeling for untargeted substructure exploration in metabolomics

(2016) Justin Johan Jozias van der Hooft et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

MSAcquisitionSimulator: data-dependent acquisition simulator for LC-MS shotgun proteomics

(2015) Dennis Goldfarb et al.   BIOINFORMATICS

JAMSS: proteomics mass spectrometry simulation in Java

(2014) R. Smith et al.   BIOINFORMATICS

Proteomics, lipidomics, metabolomics: a mass spectrometry tutorial from a computer scientist's point of view

(2014) Rob Smith et al.   BMC BIOINFORMATICS

Competitive fragmentation modeling of ESI-MS/MS spectra for putative metabolite identification

(2014) Felicity Allen et al.   Metabolomics

CFM-ID: a web server for annotation, spectrum prediction and metabolite identification from tandem mass spectra

(2014) Felicity Allen et al.   NUCLEIC ACIDS RESEARCH

LC-MS alignment in theory and practice: a comprehensive algorithmic review

(2013) R. Smith et al.   BRIEFINGS IN BIOINFORMATICS

Mspire-Simulator: LC-MS Shotgun Proteomic Simulator for Creating Realistic Gold Standard Data

(2013) Andrew B. Noyce et al.   JOURNAL OF PROTEOME RESEARCH

Toward Global Metabolomics Analysis with Hydrophilic Interaction Liquid Chromatography–Mass Spectrometry: Improved Metabolite Identification by Retention Time Prediction

(2011) Darren J. Creek et al.   ANALYTICAL CHEMISTRY

MSSimulator: Simulation of Mass Spectrometry Data

(2011) Chris Bielow et al.   JOURNAL OF PROTEOME RESEARCH

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

(2010) Tomáš Pluskal et al.   BMC BIOINFORMATICS

LC-MSsim - a simulation software for Liquid Chromatography Mass Spectrometry data

(2009) Ole Schulz-Trieglaff et al.   BMC BIOINFORMATICS

TOPPView: An Open-Source Viewer for Mass Spectrometry Data

(2009) Marc Sturm et al.   JOURNAL OF PROTEOME RESEARCH

Highly sensitive feature detection for high resolution LC/MS

(2008) Ralf Tautenhahn et al.   BMC BIOINFORMATICS