Current Proteomics - Volume 8, Issue 1, 2011

This special edition on Quantitative Mass Spectrometry in Proteomics focuses on some of the leading technologies that are currently used in state-of-the-art laboratories. In recent years, mass spectrometry-based proteomics has come a long way and seen a tremendous advancement to the point where quantitative measurements are no longer a distant goal, but have become routine to some of the leading labs. However, thi Read More

Since its introduction in 2002 ‘stable isotope labeling by amino acids in cell culture’ (SILAC) has become a major tool for quantitative proteomics. Stable isotopes are incorporated into proteins by introduction of labeled amino acids in growth medium. This methodology's compatibility with virtually all cell culture conditions, ease of implementation into existing workflows and the high quality quantitative data that can be obta Read More

Isobaric tags for absolute and relative quantification (iTRAQ) provide the quantitative proteomics community with an easy-to-use tool to examine proteome changes. Five years after the launch of the technique, has the community become familiar with iTRAQ? In this review, we propose to answer this question by looking at two of its facets. On the one hand, we enquire whether iTRAQ is used ‘optimally’; in other words, whet Read More

Multiplexed stable isotope reagents such as iTRAQ and Tandem Mass Tag (TMT) designed for MS/MS-based quantitation of peptides rely on accurate and robust detection of low mass fragments for peptide precursor ions. In the past, such analyses depended upon mass spectrometers capable of producing the so-called “triple-quadrupole-like” fragmentation including triple quadrupole mass spectrometers (TQMS) and quadrupole t Read More

The proteolytic 18O labeling method determines the relative ratios of individual proteins between two samples. This technique utilizes a protease and water (H216O and H218O) to produce labeled peptides; peptides in one sample incorporate 16O by labeling in H216O, and the other sample incorporates 18O by labeling in H218O. Both samples are mixed in a 1:1 ratio and subjected to mass spectrometric analysis to identify a Read More

Mass spectrometry has become a powerful tool for determining the composition, stoichiometry, subunit interactions, and architectural organization of non-covalent protein complexes. The vast majority of assemblies studied so far by this approach are those that contain a sufficient amount of electrostatic interactions and hydrogen bonds that can survive the transition from solution to the gas-phase and maintain the structural Read More

Organelles and compartments are distinguished by their biological functions, which in turn are reflected by their proteome profiles. Prerequisites for the organization of cellular compartments are mechanisms that help to generate and maintain their proper composition. The nucleolus is one of the compartments that have been the focus of intense research during the past years. It is now well-established that nucleoli are crucial Read More