1418 Proteomics 2009, 9, 1418–1419

Affinity-MS – Methods and applications

in proteomics research

This Special Part of the issue on “Affinity – MS” gives an overview of variousaffinity enrichment strategies used for mass spectrometry-based protein analysis.The issue focuses on the application of affinity-based separation methods that canbe used to increase the selectivity and sensitivity of mass spectrometric-basedproteomics research. The first two sections review affinity methods used for theanalysis of the plasma proteome and phosphoproteome. The third section reviewsaffinity enrichment strategies based on glycosylation or peptide ligands. Thefourth section describes strategies about unbiased immunoaffinity approacheswhich use defined sets of motif-specific capture molecules. This enables theenrichment of classes of peptides sharing the same short epitope prior to massspectrometry-based identification.

In the “Affinity enrichment strategies for mass spectrometry-based plasma pro-teomics” section, Pernemalm et al. describe different affinity-based pre-fractionationmethods which can be applied to analyse the plasma proteome. Pre-fractionationmethods are the key issue when it comes to addressing the complexity of the plasmaproteome and to looking into low abundance analytes. The authors discuss differentprotein and peptide affinity pre-fractionation methods that can be applied prior tomass spectrometric (MS) analysis and assess the performance of the different pre-fractionation methods by comparing annotated cellular and extracellular proteins ofpublicly available MS plasma proteomic data sets.

Callesen et al. review the current status of serum protein profiling involvingsolid-phase extraction and mass spectrometry methods and discuss these ap-proaches as potential diagnostics tools. For them, standardizedsample collection and processing is as important as the subsequentenrichment strategies. The authors focus on various solid-phaseextraction methods that can be used to enrich subproteomes toachieve an increase in resolution and sensitivity in the subsequentMS analysis.

The last article of this section, presented by Sparbier et al., dis-cusses MALDI MS technology with a specific focus on immunoaffi-nity enrichment. Focused immunoaffinity enrichment strategiesincrease the specificity and sensitivity of the assay and enable theidentification of disease-specific biomarkers. Appropriate internalstandard peptides enable the accurate quantitation of target analytes of interest. Thearticle closes with an outlook on the potential of MALDI-TOF MS for clinical routinediagnostics.

In the second section, which is entitled “Affinity enrichment strategies for massspectrometry-based phosphoproteomics”, Thingholm et al. describe how differentanalytical strategies can be used to analyse the dynamic changes of the phospho-proteome that occur during signal transduction processes which leads to cell prolif-eration, differentiation and apoptosis. Cell biological applications are described for

EDITORIAL

Thomas Joos

Affinity-based enrichmentstrategies are well suited to enrichtarget proteins from complexbiological samples priorto mass spectrometric analyses

© 2009 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim www.proteomics-journal.com

Proteomics 2009, 9, 1418–1419 1419

phosphoproteins or phosphopeptides affinity enrichment methods prior the massspectrometry-based analysis.

Nathan et al. focus on the quantitative analysis of the phosphoproteome to profiledrug activity and to identify disease-specific biomarkers. The paper has a specialfocus on the biological interpretation of drug action on cell signalling.

The third section entitled “Reduction of sample complexity” includes a View-point article by Bruno Domon where he describes an affinity approach based onglycosylation that can be applied to reduce sample complexity. Reduction of samplecomplexity is an important prerequisite for quantitative proteomics analyses. Arobust glycopeptide isolation method is feasible due to the chemical properties of theglycans. Such an enrichment approach reduces sample complexity and improvessensitivity of the assay. Boschetti and Righetti describe in their review the art ofobserving rare protein species in proteomes using peptide ligand libraries. Combi-natorial ligand libraries of hexapeptides are used to enrich the low-abundance pro-teome. The authors discuss the physico-chemical properties of the hexapeptidelibrary and of shorter oligopeptides and present different applications of this meth-od, including the proteome analysis of body fluids and cell lysates.

In the last section entitled “Perspectives for immunoaffinity-based enrichmentstrategies” Wingren et al. discuss a strategy for surveying the proteome using af-finity proteomics and mass spectrometry. The authors define sets of peptidemotifs that are present in sets of up to 100 different proteins. Motif-specific anti-bodies can be generated and applied in an immunoaffinity enrichment approach.The potential of this approach for global proteome analysis is discussed. A similarapproach is presented by Poetz et al. who present a concept involving group-spe-cific anti-peptide antibodies directed against short C- or N-terminal tags of targetpeptides. Such group-specific antibodies allow the enrichment of signature pep-tides sharing the same terminal epitope. Peptide classes with identical termini canbe fractionated using immunoaffinity enrichment steps and can subsequently beidentified using a mass spectrometry-based readout. Both strategies are able tocover a wide range of any given proteome with a relatively low number of anti-bodies.

In summary, affinity-based enrichment strategies are well suited to enrich targetproteins from complex biological samples prior to mass spectrometric analyses. Af-finity enrichment strategies will enable the identification of disease-specific bio-markers or patterns of biomarkers, which will finally allow the development of moreefficient diagnostics and personalised patient therapy.

Thomas JoosPROTEOMICS Editor

© 2009 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim www.proteomics-journal.com