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 Spectrometer is an analytical instrument used in Mass Spectrometry. It typically consists of several key components: Sample Inlet; Ion Source, where analyte molecules are ionized into charged particles; Mass Analyzer,which separates these ions according to their m/z values; and Detector, which measures the number and intensity of the ions. In chromatographic applications, this entire setup is often referred to as an MS detector, as it serves as the detection module connected to a chromatograph.
  • 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 calculated by dividing the mass of an ion by its charge. In most cases, ions have a charge of +1 or –1, which means the m/z value is numerically equal to the ion’s mass. However, for ions with higher charges, the m/z value will be lower than the actual mass.
  • 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 with particular m/z value 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) 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 value, 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.