Basic principles and terms

• Mass Spectrometry (MS) is an analytical detection method that determines the structure of compounds from the ions to which the compound is fragmented.
• m/z means Mass to Charge ratio. It is the value particular ions are divided by. Most common usage is the usage of ions with the charge of +1 or -1, making the m/z effectively just the mass of the ion.
• MS Detector is the device serving for the Mass Spectrometry. It generally composes of several parts - Sample Inlet, Ion Source where the compounds entering the detector are fragmented to ions, Mass Analyzer in which the particular ions are separated based on their m/z ratio and Detector, where the ions are detected.
• MS Spectrum is the basic information coming out of the MS Detector - it is a set of data describing the relative intensities of ions of particular m/z fragmented from the compound.
• Raw Data is a matrix of the spectra and the retention time.
• Total Ion Current (TIC) represents the total signal coming from the MS Detector, in fact summing all the individual ion intensity values from each spectra to single value.
• Base Peak Intensity (BPI) is another interesting signal in the MS practice - it represents the signal showing the intensity of the highest intensity ion from each spectra.
• Extracted Ion Current (EIC) is the signal over time of one single ion of selected m/z, as gained from the Raw Data.
• Raw Spectrum is a continuous spectrum (similar to the UV spectrum) of the compound - individual data points are connected by a curve.
• Stick Spectrum is a simplified version of the Raw Spectrum, where "Peaks" made by small imprecission of the MS Detector are instead represented by a single m/z value, so called Stick.