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.
  • 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.
  • Tandem Mass Spectrometry (MS-MS or MS2) is a technique using more complex version of MS Detector, where the Mass Analyzer separates the ions as usual, but rather than having the Detector next, another ionization occurs on selected ion and a second Mass Analyzer is used before detecting the outcome.
  • m/z means Mass to Charge ratio. It is the value particular ions are separated 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 Spectrum is the basic information coming out of the MS Detector - it is a set of data describing the intensities (relative or absolute) of ions of particular m/z fragmented from the compound or it's part (in case of Tandem Mass Spectrometry).
  • Raw Data is the information gained from detector in the form of collection of intensities for specific ions with particular m/z at specified retention time. Sometimes these raw data are in the form of spectra, sometimes these are just particular ions collected over time (without the spectral information).
  • 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 imprecision of the MS Detector are instead represented by a single m/z value, so called Stick.