Proteomics Glossary

Electrospray Ionization (ESI): Ionization by applying high voltage to an analyte solution, often the eluate of an HPLC column, flowing through a nano-bore spray capillary. The high potential causes the liquid to spray out of the tip as a butt of tiny, highly charged droplets. The solvent molecules evaporate and the remaining charged analyte molecule, such as a peptide or protein, enters the mass analyzer. This method of ionization is frequently coupled with HPLC (LC-MS).

Mass Spectrometer: An instrument that ionizes sample molecules and separates the ions according to their mass-to-charge (m/z) ratio. A mass spectrum is a graphical plot of measured ion abundance vs. m/z.

MS/MS: Also called tandem mass spectrometry. A technique which utilizes two stages of mass analysis. In the analysis of a peptide digest, mass of the peptide ion formed in the ion source is first measured by the mass analyzer. Then the selected ion is activated in a collision cell with a neutral gas such as Ar, and the resulting collision-induced fragment ions are analyzed by a second mass analyzer.

MS/MS spectrum: A plot of the abundance of fragment ions produced in the collision cell of the mass spectrometer vs. m/z. Masses of fragment ions can be predicted from a known sequence and are used to identify proteins with the help of bioinformatic tools. Sequence information can be obtained from the MS/MS spectrum manually if the protein is not in the searchable database (de novo sequencing).

Matrix-assisted Laser Desorption Ionization (MALDI or MALDI-TOF): Ionization technique in which the sample is co-crystallized with a matrix of small organic molecules then irradiated with a laser which causes the analyte to vaporize, passing into the mass analyzer as charged ions.

Time-of-Flight (TOF): Method of mass analysis in which ions formed are accelerated by a pulsed potential down an evacuated tube. The time of flight down the tube correlates to mass, with lighter molecules taking less time to arrive at the detector than heavier one