“…Whether they are free or commercial tools, the processing is mainly the same, although it may differ in how the steps are carried out, some of them working with in-house made algorithms. In the literature reviewed, the most employed tools were open-source software as XCMS (R package or Online) [17,18,75,76], MZmine [16,77] and MetAlign [78]; and commercial software as Mass Profiler Pro (Agilent Technologies Inc.) [79,80] , Progenesis QI (Non Linear Dynamics, Waters) [15,25,72], MarkerLynx (Waters) [81,82], SIEVE (Thermo Scientific) [37] and Compound Discoverer (Thermo Scientific) [83]. Some of them, as the open source MS-DIAL [84] or Compound Discoverer (Thermo Scientific) among others commercial tools, not only perform the abovementioned processes, but also the extraction and deconvolution of DDA and DIA spectral data and annotation by comparison of the deconvoluted MS/MS spectra with in house and/or public data bases, which is especially important for conventional DIA spectral data interpretation [49,85,86].…”