Proteome Informatics Group > Java Proteomic Library

Mass Spectrum


Mass spectrometry (MS) is used for measuring the mass, or more strictly speaking, the mass-to-charge ratio (m/z), of the components in a sample.

A mass spectrum is the result of mass detection and acquisition of a ionized sample in a spectrometry experiment. It is a diagram, with m/z along the horizontal axis and the intensity of the signal for each component along the vertical axis.

A mass spectrum can be presented as raw data or as a peak list. The peak list is a processed form of the raw data and is the only data jpl is based on.

List of peaks

In its simplest form, it contains a list of m/z values of the detected peptides. Most peak list formats, however, also include the intensity value and possibly other data (for instance, charge state), for each of the detected peptides.

Here how we build peak list in the jpl:

	double[] mzs = new double[] {1.1, 2.2, 3.3, 4.4, 5.5, 6.6};
	// classic peak list
	JPLIPeakList peakList = new JPLMSPeakList.Builder(mzs).build();

	// built from another peak list
	subSpec =
	    new JPLMSPeakList.Builder(peakList).indices(new int[] {2, 3})

Peak list is also wrapped in mass spectrum object.

Mass Spectrum

We have define a generic object that can store informations about any mass spectrum coming from MS, MS/MS, LC/MSMS experiments and even annotated spectra.

It contains mainly the peak list data including an m/z value and an intensity for each peak. We also have additional data from the raw data peak, such as base peak mz and intensity and data specific to spectrometer experiment type.

Mass spectrum objects are directly linked to MS parsers from where we decide to keep the set of informations:


  • the spectrum title
  • the scan number
  • the peak list
  • the ms level


  • the retention time
  • the base peak intensity


  • the parent spectrum scan number
  • the fragmented precursor
  • the fragmentation method

MS Run Statistics

JPLMSRunStats object register data coming from iterator over experimental spectrum.