Quadrupole ion traps and a new era of evolution (Proteomics)

1. Introduction For the first 30 years of their existence, three-dimensional (3D) quadrupole ion traps remained a specialty tool for a relatively few physicists and even fewer chemists (March and Hughes, 1989). These devices were ideal to study the fundamental properties of ions since the ions remained trapped in space for comparatively long amounts of […]

Nano-MALDI and Nano-ESI MS (Proteomics)

1. Introduction In line with the rapid development of miniaturized and chip-integrated approaches to analytical and bioanalytical systems, the proteomics work scheme has also been the focus of dimensional reduction. The driving arguments for miniaturization are seen in the possibilities of improved sample throughput, reduced sample volume requirements, lower reagent costs, and improved limits of […]

Hybrid MS (Proteomics)

1. Hybrid MS instruments Tandem mass spectrometry, or MS/MS, has become the preferred technology for many applications in which mass spectrometry plays a part. First, tandem mass spectrometry allows selection and isolation of specific compounds of interest and their subsequent identification. Second, the extra selectivity of MS/MS enables this technology to be used for quantification […]

Protein fingerprinting (Proteomics)

1. Introduction Identification of proteins by searching protein sequence collections with peptide mass fingerprinting data is widely used (Figure 1). The proteins in the sample are first separated to obtain one or a few proteins of interest. These proteins are then digested with a proteolytic enzyme. Mass spectra of the resulting peptide mixtures are acquired. […]

Multidimensional liquid chromatography tandem mass spectrometry for biological discovery (Proteomics)

1. Introduction The goal of biological studies is to connect genes and proteins to specific processes. In the past, dissection of biological processes entailed detailed and focused studies of a specific gene or protein. The availability of complete genome sequences has made possible broader studies to dissect the functions of proteins and genes in entire […]

Handling membrane proteins (Proteomics)

1. Introduction In spite of their vital importance to many cellular functions, we remain remarkably ignorant of membrane protein composition. Two major classes of membrane proteins exist: integral membrane proteins, which are embedded in the lipid bilayer, and the so-called peripheral membrane proteins, which are associated noncovalently with integral proteins or membrane lipid head groups […]

Sample preparation for MALDI and electrospray (Proteomics)

1. Introduction The development of electrospray (ESI) and matrix-assisted laser desorption/ ionization (MALDI) in the early 1990s built upon the advances made by fast atom bombardment (FAB). FAB allowed the analysis of biomolecules previously intractable to mass spectrometric analysis, without derivatization. The subsequent development of MALDI and ESI provided increased sensitivity while significantly increasing the […]

Improvement of sequence coverage in peptide mass fingerprinting (Proteomics)

1. Introduction Detailed information regarding the presence of isoforms, splice variants, and posttranslational modifications (PTMs) is essential for the complete understanding of the biological function, location, and properties of a specific protein. Traditionally, proteomic studies are based on protein separation using two-dimensional (2D) gel electrophoresis followed by identification by mass spec-trometry (MS). An alternative strategy […]

Tutorial on tandem mass spectrometry database searching (Proteomics)

1. Introduction With recent advances in search software and available databases, a novice can now easily perform a tandem mass spectrometry (MS/MS) sequence database search. Such a search requires an input spectrum, a sequence database to query, and a set of search parameters to guide the search. This tutorial will cover the mechanisms of performing […]

Techniques for ion dissociation (fragmentation) and scanning in MS/MS (Proteomics)

1. Introduction Modern mass spectrometry techniques such as electrospray ionization (ESI) and atmospheric pressure chemical ionization (APCI) often only produce ions representing the intact molecule, usually protonated molecules (MH+). Even when the mass of these ions is measured to an accuracy that will allow for a determination of the elemental composition, the identity of the […]