Quantitative Glycoproteomics

Living reference work entry

Abstract

The term “proteome” was coined by Wilkins et al. (1995) to describe the protein complement of the genome. The term “proteomics” was first used to describe the complexity of proteins expressed in an organism using two-dimensional gel electrophoresis (2-DE) followed by quantitative analysis. 2-DE remains the highest-resolution protein separation method available, but the ability to concentrate and identify low-abundance proteins has always been an extremely difficult problem. Mass spectrometry (MS) has been an integral part of approaching this problem (de Hoog and Mann 2004; Lane 2005). Although improvements in 2-D gel technology have been made since its introduction, three enabling technological advances have provided the basis for the foundation of the field of proteomics (Patterson 2000). The first advance was the introduction of large-scale nucleotide sequencing of both expressed sequence tags (ESTs) and genomic DNA. The second was the development of mass spectrometers able to ionize and mass-analyze biological molecules and the widespread introduction of mass spectrometers, capable of data-dependent ion selection for fragmentation (MS/MS) (i. e., without the need for user intervention). The third was the development of computer algorithms able to match uninterpreted (or partially interpreted) MS/MS spectra with translations of the nucleotide sequence databases, thereby tying together the first technological advances. The mass spectrometer instruments are named for their type of ionization source and mass analyzer (Patterson and Aebersold 1995; Carr and Annan 1997; Patterson 1998). To measure the mass of molecules, the test material must be charged (ionized) and desolvated. The two most successful mechanisms for ionization of peptides and proteins are matrix-assisted laser desorption ionization (MALDI) and electrospray ionization (ESI). In MALDI, the analyte of interest is embedded in a matrix that is dried and then volatilized in a vacuum under ultraviolet laser irradiation. This is a relatively efficient process that ablates only a small portion of the analyte with each laser shot. Typically, the mass analyzer coupled with MALDI is a time-of-flight (TOF) mass analyzer that measures the elapsed time from acceleration of the charged (ionized) molecules through a field-free drift region (Kowalski and Stoerker 2000). The other common ionization source is ESI, in which the analyte is sprayed from a fine needle at high voltage toward the inlet of the mass spectrometer (which is under vacuum) at a lower voltage. The spray is typically either from a reversed-phase HPLC column or a nanospray device (Wilm and Mann 1994), similar to a microinjection needle. The ions formed during this process are directed into the mass analyzer, which could be a triple-quadrupole, an ion trap, a Fourier-transform ion cyclotron resonance (FT-ICR), or a hybrid quadrupole TOF (Qp-TOF) type (Morris et al. 1996). Although unambiguous identification of a protein cannot always be derived from the masses of a few of its peptides in the tandem mass spectrometer, peptide ions from the first mass spectrometer run are fragmented and identified in a second run to yield a more valuable commodity of a peptide sequence.

Keywords

Mass Analyzer Tandem Mass Spectrometer Nucleotide Sequence Database Quantitative Proteomics Widespread Introduction 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2015

Authors and Affiliations

  1. 1.Georgetown University Hospital, Georgetown LombardiWashingtonUSA

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