Apparatus, methods, and computer readable media having computer code for calibrating chromatograms to achieve chromatographic peak shape correction, noise filtering, peak detection, retention time determination, baseline correction, and peak area integration. A method for processing a chromatogram, comprises obtaining at least one actual chromatographic peak shape function from one of an internal standard, an external standard, or an analyte represented in the chromatogram; performing chromatographic peak detection using known peak shape functions with regression analysis; reporting regression coefficients from the regression analysis as one of peak area and peak location; and constructing a calibration curve to relate peak area to known concentrations in the chromatogram. A method for constructing an extracted ion chromatogram, comprises calibrating a low resolution mass spectrometer for both mass and peak shape in profile mode; performing mass spectral peak analysis and reporting both mass locations and integrated peak areas; specifying a mass defect window of interest; summing up all detected peaks with mass defects falling within the specified mass defect window to derive summed intensities; and plotting the summed intensities against time to generate a mass defect filtered chromatogram.