patRoon: open source software platform for environmental mass spectrometry based non-target screening

R: A Language and Environment for Statistical Computing

R Core Team · 2000 · 352.8K citations · Full text

XCMS:  Processing Mass Spectrometry Data for Metabolite Profiling Using Nonlinear Peak Alignment, Matching, and Identification

Colin A. Smith, Elizabeth J. Want, Grace O’Maille et al. · Analytical Chemistry · 2006 · 5K citations

Engineering, Biological Mass Spectrometry, Metabolomic Profiling +24

<i>circlize</i>implements and enhances circular visualization in R

Zuguang Gu, Lei Gu, Roland Eils et al. · Bioinformatics · 2014 · 4.3K citations · Full text

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

Tomáš Pluskal, Sandra Castillo, Alejandro Villar‐Briones et al. · BMC Bioinformatics · 2010 · 3.8K citations · Full text

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

Hiroshi Tsugawa, Tomáš Čajka, Tobias Kind et al. · Nature Methods · 2015 · 3.2K citations · Full text

Biochemistry, Medicine, Mass Spectrometry +7