Glossary of Terms in Mass Spectrometry     

Average molecular weight : The mass of a molecule of a given empirical formula calculated using the average atomic weights for each element.  An average mass is obtained in MALDI-TOF-MS when a peak in not isotopically resolved.    

Monoisotopic molecular weight : The mass of a molecule containing only the most abundant isotopes, calculated with exact atomic weights.  With respect to peptide analysis, the monoisotopic peak is the 12C peak, ie the first peak in the peptide isotopic envelope.

Background subtraction : The process in which the background (chemical and detector noise) is subtracted, leaving the peaks above the noise at the base level.

Base peak : The most intense peak in a mass spectrum.  A mass spectrum is usually normalized so that this peak has an intensity of 100 %.

Calibrant : A compound used for the calibration of an instrument.

Calibration : A process where known masses are assigned to selected peaks.  The purpose is to improve the mass accuracy of an MS instrument.

Centroided mass peak : The centroided mass peak is located at the weighted centre of mass of the profile peak.

Collision induced dissociation (CID) : A process whereby an ion of interest, the precursor ion , is selected, isolated , excited and fragmented by collision with an inert gas within the mass spectrometer.

Dalton (Da) : According to the guidelines of the SI, the use of the term Dalton defined as 1/12 of the mass of a carbon 12 atom( 1 Da = 1,6601x10-27 kg ) is no longer recommended.  However it is still a current unit in biochemistry.

Daughter ion (see product or fragment ion): An ion resulting from CID performed on a precursor ion during a product ion MS/MS spectrum.

Digestion : Cleavage of subject protein by proteolytic enzymes, including trypsin and chymotrypsin.

Dried droplet method : Sample preparation method for MALDI-TOF MS applicable to peptides, protein digests and full length proteins.

Electrospray ionisation (ESI) : An ionisation technique, which enables the formation of ions from molecules directly from samples in solution.  The ions formed in this process are predominantly multiply charged.  Commonly coupled with analyzers capable of tandem mass spectrometry (MS/MS).  It is readily coupled with HPLC and capillary electrophoresis.

Expression proteomics : The massive parallel study of highly heterogeneous protein mixtures with high throughput techniques like 2-D electrophoresis and MALDI mass spectrometry.

External calibration :  A calibration is performed with a known calibrant mixture.  The resultant calibration constants (file) are then applied to a separate sample.

Fragmentation : A physical process of dissociation of molecules into fragments in a mass spectrometer.  The resultant spectrum of fragments is unique to the molecule or ion.  For example, fragmentation data can be used to sequence peptides and resultantly provide data for protein identification.

Full length protein : An intact polypeptide chain, constituting a protein in its native or denaturated state.  The molecular weight of which can be determined accurately with MALDI and ESI-MS.

Functional proteomics : This research is only possible with non-denaturated cell extracts and requires different tools than 2D electrophoresis and MALDI-MS.  A smaller subset of proteins is isolated from the highly heterogeneous protein lysate and analyzed with mils techniques that do not affect protein complexes and three-dimensional structures.

Immobilized pH gradients : Polyacrylamide gels,which contain an in-built pH gradient, created by acrylamide derivatives, which arry acidic and buffering groups.  Because an immobilized pH gradient is absolutely continuous, narrow pH intervals can be prepared which allow unlimited resolution.

In-gel-digestion : The embedded protein in the gel is cleaved using enzymes of known specificity. During the process, peptides are formed, which are extracted from the gel for subsequent analysis.

Internal calibration : Calibration where known masses in each spectrum are used to calibrate that spectrum.  Greater mass accuracy than an external calibration.

Ion detector : A detector that amplifies and converts ions into an electrical signal.

Ion gate : Typically an electrical deflector that permits certain ions through to later stages of ion optics (open), or deflects unwanted ions out of the way of the later stages of the mass spectrometer.  Commonly used in post-source decay (PSD) analysis for the selection of precursor ion.

Ion source : Region of the mass spectrometer where gas phase ions are produced.

Ion transmission efficiency : Refers to the fraction of the ions produced in the source region that actually reaches the detector.

Ionisation : The process of converting a sample molecule into an ion in a mass spectrometer.

Isoelectric point (pI) : The pH value where the net charge of an amphoteric substance is zero. Because the pK values of buffering groups are temperature dependent, this is valid also for the pI.

Isotope : Atoms of the same element having different mass numbers due to differences in the number of neutrons.

Isotope abundance: The relative amount in nature of certain atomic isotopes.

Linear time-of-flight mass analyzer : Simplest TOF analyzer, consisting of a flight tube with an ion source at one end and a detector at the other.

Mass accuracy : The ability to assign the actual mass of an ion. This is typically expressed as an error value.

Mass analyzer : Second part of the mass spectrometer, separating the ions formed in the ion source according to their m/z value.  Examples of mass analyzers include ion trap, quadrupole, time of flight and magnetic sector.