Mahmoud Hamdan

Reduction and alkylation of proteins in preparation of two-dimensional map analysis: why, when, and how?

The standard procedure adopted up to the present in proteome analysis calls for just reduction prior to the isoelectric focusing/immobilized pH gradient (IEF/IPG) step, followed by a second reduction/alkylation step in between the first and second dimension, in preparation for the sodium dodecyl sulfate‐polyacrylamide gel electrophoresis (SDS‐PAGE) step. This protocol is far from being optimal. It is here demonstrated, by matrix assisted laser desorption/ionization‐time of flight (MALDI‐TOF)‐mass spectrometry, that failure to reduce and alkylate proteins prior to any electrophoretic step (including the first dimension) results in a large number of spurious spots in the alkaline pH region, due to “scrambled” disulfide bridges among like and unlike chains. This series of artefactual spots comprises not only dimers, but an impressive series of oligomers (up to nonamers) in the case of simple polypeptides such as the human α‐ and β‐globin chains, which possess only one (α‐) or two (β‐) ‐SH groups. As a result, misplaced spots are to be found in the resulting two‐dimensional (2‐D) map, if performed with the wrong protocol. The number of such artefactual spots can be impressively large. In the case of analysis of complex samples, such as human plasma, it is additionally shown that failure to alkylate proteins results in a substantial loss of spots in the alkaline gel region, possibly due to the fact that these proteins, at their pI, regenerate their disulfide bridges with concomitant formation of macroaggregates which become entangled with and trapped within the polyacrylamide gel fibers. This strongly quenches their transfer in the subsequent SDS‐PAGE step.

Alkylation kinetics of proteins in preparation for two-dimensional maps: a matrix assisted laser desorption/ionization-mass spectrometry investigation.

All existing protocols for protein separation by two‐dimensional (2‐D) gel electrophoresis require the full reduction, denaturation, and alkylation as a precondition for an efficient and meaningful separation of such proteins. Existing literature provides a strong evidence to suggest that full reduction and denaturation can be achieved in a relatively short time; the same thing, however, can not be said for the alkylation process, which the present study shows that more than 6 h are required for a complete alkylation. We have used matrix assisted laser desorption/ionisation‐time of flight‐mass spectrometry (MALDI‐TOF‐MS) to monitor protein alkylation by iodoacetamide over the period 0 – 24 h at pH 9. The present, fast and specific MS method provided clear indication on the extent and speed of alkylation which reached ∼70% in the first 2 min, yet the remaining 30% resisted complete alkylation up to 6 h. The use of sodium dodecyl sulfate (SDS) during the alkylation step resulted in a strong quenching of this reaction, whereas 2% 3‐[(3‐cholamidopropyl)dimethylammonio]‐1‐propanesulfonate (CHAPS) exerted a much reduced inhibition. The implications of the present measurements on 2‐D gel analysis in particular and proteomics in general are discussed.

Quantitative Proteomics: A Review of Different Methodologies

The present review attempts to cover the vast array of methods which have appeared in the last few years for performing quantitative proteome analysis. These methods are divided into two classes: those applicable to conventional two-dimensional map analysis, coupling orthogonally a charge-based step (isoelectric focusing) to a size-based separation [sodium dodecylsulfate (SDS)-electrophoresis] and those applicable to two-dimensional chromatographic protocols. The first method, although being by and large the most popular approach, can offer differential display of paired samples with relatively few methods, the oldest one being based on statistical analysis performed on sets of gels via powerful software packages, such as the MELANIE, PDQuest, Z3 and Z4000, Phoretix and Progenesis. Recent developments comprise analysis performed on a single gel containing mixed samples differentially labeled, either with fluorophors (Cy3 and Cy5) or with d0/d3 acrylamide. Conversely, chromatographic approaches, which mostly rely on analysis not of intact proteins but of their tryptic digests, offer a panoply of differential labeling protocols, most of which rely on stable isotope tagging. Essentially, all possible reactions have been described, such as those involving Lys, Asp, Glu, Cys residues, as well as a number of methods exploiting differential derivatization of amine and carboxyl groups generated during proteolysis. All such methods are described and evaluated.

Proteomic analysis of rat hippocampus after repeated psychosocial stress

Since stress plays a role in the onset and physiopathology of psychiatric diseases, animal models of chronic stress may offer insights into pathways operating in mood disorders. The aim of this study was to identify the molecular changes induced in rat hippocampus by repeated exposure to psychosocial stress with a proteomic technique. In the social defeat model, the experimental animal was defeated by a dominant male eight times. Additional groups of rats were submitted to a single defeat or placed in an empty cage (controls). The open field test was carried out on parallel animal groups. The day after the last exposure, levels of hippocampal proteins were compared between groups after separation by 2-D gel electrophoresis and image analysis. Spots showing significantly altered levels were submitted to peptide fingerprinting mass spectrometry for protein identification. The intensity of 69 spots was significantly modified by repeated stress and 21 proteins were unambiguously identified, belonging to different cellular functions, including protein folding, signal transduction, synaptic plasticity, cytoskeleton regulation and energy metabolism. This work identified molecular changes in protein levels caused by exposure to repeated psychosocial stress. The pattern of changes induced by repeated stress was quantitatively and qualitatively different from that observed after a single exposure. Several changed proteins have already been associated with stress-related responses; some of them are here described for the first time in relation to stress.

Protein alkylation in the presence/absence of thiourea in proteome analysis: a matrix assisted laser desorption/ionization-time of flight-mass spectrometry investigation.

Although it is highly recommended that reduction and alkylation of free –SH groups in proteins should be performed prior to any electrophoretic step (including the first isoelectric focusing/immobilized pH gradient (IEF/IPG) dimension), it is here reported that one component of the sample solubilization cocktail adopted recently (namely thiourea) strongly quenches such alkylation process (as typically carried out with iodoacetamide, IAA).The present matrix assisted laser desorption/ionization‐time of flight‐mass spectrometry (MALDI‐TOF‐MS) analysis demonstrates that thiourea is an effective scavenger of IAA, since its sulfur atom reacts as efficiently as the ionized, free –SH group of Cys in proteins at alkaline pH values (pH 8.5–9.0). As a result of this reaction, free IAA is quickly depleted by thiourea, via the formation of an intermediate adduct, which is rapidly deamidated to form the cyclic compound thiazolinidone monoimine. This reaction strongly competes with the direct addition reaction of IAA onto the –SH group in proteins, resulting in poorly alkylated proteins. It is, therefore, recommended that, whenever possible and compatible with the type of sample, thiourea should be omitted from the solubilizing cocktail in proteome analysis. However, after proper sample reduction and alkylation, thiourea can be incorporated into the IEF/IPG gel, where it will have the beneficial effect of augmenting protein solubility at their pI values and scavenging the excess of free IAA.

Supercritical fluid chromatography coupled to electrospray mass spectrometry: a powerful tool for the analysis of chiral mixtures.

Supercritical fluid chromatography coupled to a hybrid mass spectrometer (Q-Tof2) equipped with electrospray ion source has been used to separate and characterise a wide range of pharmaceutical racemates. We have chosen diverse molecular structures to demonstrate the potential of such experimental arrangement for high throughput analyses. The use of three different chiral stationary phases and different pressure/temperature working conditions provided clear indications on how such a high throughput method can be developed. The use of mass spectrometry was found to be essential for an unambiguous assignment of the eluting components particularly in the case of complex mixtures. The direct coupling of both systems without the need for a special interface resulted in similar peak shapes and peak widths in the UV and total ion current (TIC) chromatograms.

Effect of experimental conditions on the analysis of sodium dodecyl sulphate polyacrylamide gel electrophoresis separated proteins by matrix-assisted laser desorption/ ionisation mass spectrometry.

Two mixtures of proteins having molecular weights in the range approximately 8-97 kDa were separated by sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE) and examined by delayed extraction matrix-assisted laser desorption/ionisation mass spectrometry (MALDI-MS). Part of our aim in this study is to gain more insight into the influence of the various experimental conditions on the overall quality of the acquired mass spectral data. Different protein extraction procedures, two staining agents, and extraction times, were among the parameters assessed. In terms of the overall quality of the acquired mass spectra and the speed of protein recovery, ultrasonic assisted passive elution, into a solvent mixture containing formic acid/acetonitrile/2-isopropanol/water, was found to be more efficient than other elution procedures. The higher resolution associated with the delayed extraction mode allowed the identification of a number of protein modifications, including multiple formylation provoked by formic acid, cysteine alkylation caused by unpolymerised acrylamide monomers, and complexation with the staining reagents. The detection of these modifications, however, was limited to proteins under 30 kDa. Analysis of a ubiquitin tryptic digest by reflectron MALDI time-of-flight (TOF) allowed reliable identification of a number of the formylation sites.

Protein alkylation by acrylamide, its N-substituted derivatives and cross-linkers and its relevance to proteomics: A matrix assisted laser desorption/ionization-time of flight-mass spectrometry study

The present review highlights some important alkylation pathways of proteins, as measured by matrix assisted laser desorption/ionization‐time of flight (MALDI‐TOF)‐mass spectrometric analysis, engendered by acrylamide and a number of its derivatives, including N‐substituted acrylamides, cross‐linkers and Immobilines (the acrylamido weak acids and bases used to create immobilized pH gradients). The present data are of relevance in two‐dimensional maps and proteome analysis. It is shown that acrylamide can alkylate the –SH group of proteins even when engaged in disulfide bridges. An order of reactivity is obtained for a series of cross‐linkers, which are shown to have an extremely reacting double bond, with the second one almost unreactive, originating “pendant, unreacted ends”, which can subtract proteins migrating in a gel by covalently affixing them to it. An analogous reactivity scale is constructed also for the Immobiline chemicals, whose reactivity is shown to be linearly dependent on the pK values, the least reacting species being the acidic compounds. When analyzing real‐life samples by two‐dimensional (2‐D) maps, like milk powders, a number of modifications can be detected by MALDI‐TOF mass spectra of eluted spots, including variable phosphorylation sites (up to nine) and lactosyl moieties. If, for eluting such spots, formic acid is used, MALDI‐TOF mass spectrometry (MS) reveals an incredible number of formylation sites, on Ser and Thr residues.

Two-dimensional gel electrophoresis/matrix-assisted laser desorption/ionisation mass spectrometry of a milk powder.

Proteins in a commercial milk powder have been separated by two-dimensional gel electrophoresis and analysed by matrix-assisted laser desorption ionisation mass spectrometry. The mass spectrometric analyses were conducted in two steps: analysis of the intact proteins following their passive extraction into a suitable solvent mixture and analysis in reflectron mode of in situ digests of a number of gel spots. The combination of the two methods allowed a reliable identification of a number of proteins, including nine caseins as well as certain protein modifications including single/multiple phosphorylation, lactose-protein conjugates and Coomassie Brilliant Blue adducts. Analyses of the intact proteins prior to their in situ digestion contributed to a more efficient and reliable consultation of protein databases.

Probing the reactivity of S-S bridges to acrylamide in some proteins under high pH conditions by matrix-assisted laser desorption/ ionisation.

There is compelling evidence to suggest that cysteine-acrylamide adduct formation is a modification experienced by proteins separated by two-dimensional (2-D) gel electrophoresis. Whether the -SH group involved in such complexation is offered by a free or initially disulphide-linked cysteine residue remains an open question. To address this question a number of proteins containing free and/or disulphide-linked cysteine (Cys) residues have been incubated with acrylamide monomer and examined by delayed extraction matrix-assisted laser desorption/ionisation time-of-flight (MALDI-TOF). These data provide strong evidence to suggest that the presence of free Cys in the investigated proteins is not the most important requirement for the observation of Cys-acrylamide adducts. Unambiguous confirmation of this deduction was obtained by analysing the tryptic digests of the same proteins by reflectron MALDI-TOF. The assignment of the adduction sites was facilitated by the mass accuracy attained for the monitored tryptic fragments and their agreement with the corresponding predicted masses reported in the Swiss-Prot database. The same data suggest that at high pH the cysteine pairing is flexible enough to allow initially S-S linked residues to complex with acrylamide. It is also plausible that the -NH(2) terminal blockage so often encountered in proteins electroblotted from 2-D maps could originate from carbamylation, and might not have anything to do with alkylation by free, unreacted acrylamide in polyacrylamide gels.