Setting appropriate bin sizes to aggregate hyphenated high-resolution mass spectrometry data, belonging to similar mass over charge (m/. z) channels, is vital to metabolite quantification and further identification. In a high-resolution mass spectrometer when mass accuracy (ppm) varies as a function of molecular mass, which usually is the case while reading m/. z from low to high values, it becomes a challenge to determine suitable bin sizes satisfying all m/. z ranges. Similarly, the chromatographic process within a hyphenated system, like any other controlled processes, introduces some process driven systematic behavior that ultimately distorts the mass chromatogram signal. This is especially seen in liquid chromatogram-mass spectrometry (LC-MS) measurements where the gradient of the solvent and the washing step cycle-part of the chromatographic process, produce a mass chromatogram with a non-uniform baseline along the retention time axis. Hence prior to any automatic signal decomposition techniques like deconvolution, it is a equally vital to perform the baseline correction step for absolute metabolite quantification. This paper will discuss an instrument and process independent solution to the binning and the baseline correction problem discussed above, seen together, as an effective pre-processing step toward liquid chromatography-high resolution-mass spectrometry (LC-HR-MS) data deconvolution. © 2012 Elsevier B.V..