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Table 1 Overview of commonly used open-source or open-access software tools to implement NTA workflows

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

  HRMS Features Annotation Interface Language OS License References
Pre-process Find Group1 Clean-up Suspects MS extr2 Formula Comp pred3 Comp lib3 Hom extr4 Group5 Clean-up RT pred6
a CFM-ID         X X      CLI, Web C++ Cross LGPLv2.1 [30, 31]
b enviMass, enviPick, nontarget Xi X X X X      X X    GUI, R, Web R Cross GPLv3.07 [32,33,34]
c GenForm        X        CLI C++ Cross8 LGPLv2.0 [35]
d MetFrag         X X    X X CLI, R, Web Java Cross LGPLv2.0 [36]
e FOR-IDENT         Xd X     X Web HTML Cross Closed [37]
  X X X X X X X X   X    CLI, GUI C# Win LGPLv3.0 [38, 39]
g MZmine X Xgl X X X X X Xk X   Xgl    GUI Java Cross GPLv2.0 [40]
h OpenMS Xhi X X    X   Xk X   X    CLI, GUI, Python C++ Win, Lin, Mac BSD/3-Clause [41]
i ProteoWizard X              CLI, GUI C++ Win, Lin Apache 2.0 [23]
j RAMClustR       X      X    R R Cross GPLv2.0 [42]
k SIRIUS and CSI:FingerID        X X     X   CLI, GUI Java Cross GPLv3.0 [43,44,45,46,47]
l XCMS and CAMERA   X X X        X    R R Cross GPLv2.0 [48, 49]
m XCMS Online X Xl Xl    X    X   X    Web R Cross Closed [50]
n patRoon Xhi Xbhl Xhl X X X Xck Xdk Xd Xb Xjl X Xd R R Cross GPLv3.0  
  1. (1): Group features across samples; (2): automatic MS data extraction for annotation purposes; (3): Compound annotation (in silico/library); (4): unsupervised homologous series extraction; (5): grouping and annotating chemically related features (e.g. adducts, isotopes, in-source fragments); (6): retention time prediction; (7): enviMass is distributed commercially; (8): Only Microsoft Windows binaries are distributed
  2. CLI command-line interface, GUI graphical user interface, Web interfaced via internet browser, OS supported operating systems, Win Microsoft Windows, Lin GNU/Linux, Mac macOS, Cross cross-platform
  3. Italic: functionality integrated in patRoon
  4. Superscript: implemented with algorithms by given rows (omitted if only native)