Special issue in quantitative mass spectrometric proteomics

Abstract

Proteomics research has increased exponentially since the 1980s upon the simultaneous and continuous development of biochemical purification and chromatography separation techniques, ionisation sources, fast scanning high mass accuracy mass spectrometers and bioinformatic tools. Completion of the human genome project in 2003 was instrumental in advancing research in this field by creating access to more complete protein sequence information. In order for molecules to be analysed by mass spectrometry, they have to be ionised in an ionisation source prior to entering the mass spectrometer. In 2002, Koichi Tanaka and John Fenn jointly won the Nobel Prize in chemistry for the development of matrix-assisted laser desorption ionisation (MALDI) and electrospray ionisation (ESI) sources, respectively. In the 1980s Koichi Kanaka, Franz Hillencamp, and Michael Karas discovered that amino acids, proteins, and polypeptides could be ionised in a solid phase when mixed with a matrix and organic solvent, and laser ablated into a mass spectrometer (Karas et al. 1985; Tanaka et al. 1988; Hillenkamp et al. 1991; Beavis and Chait 1996). MALDI was particularly useful for the analysis of proteins subjected to endopeptidase digestion that generates peptides of specific mass, which can then be compared to a protein or genomic database to determine the identity of the protein (Yates et al. 1993; Cottrell 1994). This analysis is termed peptide mass finger printing (PMF). The concurrent development of electrospray ionisation (ESI) sources facilitated the analysis of biological macromolecules in liquid phase (Whitehouse et al. 1985). In this method molecules are ionised upon the application of a voltage to a capillary. In the charging process molecules are desolvated by electrospray dispersion and enter the mass spectrometer. ESI enabled the online analysis of molecules, including proteins and peptides, separated and purified by liquid chromatography. Development of nanoscale high performance liquid chromatography (nanoHPLC) meant that samples in the femtomole range could be analysed thereby significantly increasing analytical sensitivity. In addition, during the last decade major technological improvements of mass spectrometers have been made. In particular, the development of Thermofisher’s hybrid linear ion trap/orbitrap mass spectrometers and new generation Q-TOFs in 2005 was a breakthrough. These instruments fast-scan and measure the mass of ions with a mass accuracy at sub part per million levels significantly increasing the amount of ions that could be analysed and the sensitivity of their detection. These improvements led to a more accurate analysis of complex samples. Today in mass spectrometry these analyses are performed not only on the MS level where accurate masses of peptides are measured, but also on the tandem MS (MS/MS) level where peptides or proteins are fragmented in the gas-phase into various lengths mainly between amino acid residues that enable the determination of their sequence from either the N or C-termini. The resulting masses from MS and MS/ MS fragment ions spectra are matched with a protein sequence database with bioinformatic search engines. With all these ground-breaking advances, most of today’s biological mass spectrometrists work on developing applications while hardware improvements is now largely the realm of biotechnology companies. K. Barnouin (&) Protein Analysis and Proteomics Laboratory, Clare Hall Laboratories, London Research Institute, Cancer Research UK, Potters Bar, Hertfordshire EN6 3LD, UK e-mail: karin.barnouin@cancer.org.uk