High-accuracy mass measurement as a tool for studying proteins

How mass spectrometry can be exploited to study AMPK

AMP-activated protein kinase (AMPK) is a key regulator of metabolism and a recognised target for the treatment of metabolic diseases such as Type 2 diabetes (T2D). Here, we review how mass spectrometry (MS) can be used to study short-term control by AMPK via protein phosphorylation and long-term control due to changes in protein expression. We discuss how MS can quantify AMPK subunit levels in tissues from different species. We propose hydrogen-deuterium exchange (HDX)-MS to investigate molecular mechanisms of AMPK activation and thermoproteomic profiling (TPP) to assess off-target effects of pharmacological AMPK activators/inhibitors. Lastly, because large MS data sets are generated, we consider different approaches that can be used for their interpretation.

Subunit mass analysis for monitoring multiple attributes of monoclonal antibodies

RATIONALE

Multi-Attribute Methods (MAMs) are appealing due to their ability to provide data on multiple molecular attributes from a single assay. If fully realized, such tests could reduce the number of assays required to support a product control strategy while providing equivalent or greater product understanding relative to the conventional approach. In doing so, MAMs have the potential to decrease development and manufacturing costs by reducing the number of tests in a release panel.

METHODS

In this work, we report a MAM which is based on subunit mass analysis.

RESULTS

The MAM assay is shown to be suitable for use as a combined method for identity testing, glycan profiling, and protein ratio determination for co-formulated monoclonal antibody (mAb) drugs. This is achieved by taking advantage of the high mass accuracy and relative quantification capabilities of intact mass analysis using quadrupole time-of-flight mass spectrometry (Q-TOF MS). Protein identification is achieved by comparing the measured masses of light chain (LC) and heavy chain (HC) mAbs against their theoretical values. Specificity is based on instrument mass accuracy. Glycan profiling and relative protein ratios are determined by the relative peak intensities of the protein HC glycoforms and LC glycoforms, respectively. Results for these relative quantifications agree well with those obtained by the conventional hydrophilic interaction liquid chromatography (HILIC) and reversed-phase LC methods.

CONCLUSIONS

The suitability of this MAM for use in a quality control setting is demonstrated through assessment specificity for mAb identity, and accuracy, precision, linearity and robustness for glycan profiling and ratio determination. Results from this study indicate that a MAM with subunit mass analysis has the potential to replace three conventional methods widely used for mAb release testing including identification assay, glycosylation profiling, and ratio determination for co-formulated mAbs.

Thiol-ene Monolithic Pepsin Microreactor with a 3D-Printed Interface for Efficient UPLC-MS Peptide Mapping Analyses

To improve the sample handling, and reduce cost and preparation time, of peptide mapping LC-MS workflows in protein analytical research, we here investigate the possibility of replacing conventional enzymatic digestion methods with a polymer microfluidic chip based enzyme reactor. Off-stoichiometric thiol-ene is utilized as both bulk material and as a monolithic stationary phase for immobilization of the proteolytic enzyme pepsin. The digestion efficiency of the, thiol-ene based, immobilized enzyme reactor (IMER) is compared to that of a conventional, agarose packed bed, pepsin IMER column commonly used in LC-MS based protein analyses. The chip IMER is found to rival the conventional column in terms of digestion efficiency at comparable residence time and, using a 3D-printed interface, be directly interfaceable with LC-MS.

The emerging role of native mass spectrometry in characterizing the structure and dynamics of macromolecular complexes

Mass spectrometry (MS) is a powerful tool for determining the mass of biomolecules with high accuracy and sensitivity. MS performed under so-called "native conditions" (native MS) can be used to determine the mass of biomolecules that associate noncovalently. Here we review the application of native MS to the study of protein-ligand interactions and its emerging role in elucidating the structure of macromolecular assemblies, including soluble and membrane protein complexes. Moreover, we discuss strategies aimed at determining the stoichiometry and topology of subunits by inducing partial dissociation of the holo-complex. We also survey recent developments in "native top-down MS", an approach based on Fourier Transform MS, whereby covalent bonds are broken without disrupting non-covalent interactions. Given recent progress, native MS is anticipated to play an increasingly important role for researchers interested in the structure of macromolecular complexes.

Matrix-assisted laser desorption/ionization time of flight (MALDI-TOF) mass spectrometric analysis of intact proteins larger than 100 kDa

Effectively determining masses of proteins is critical to many biological studies (e.g. for structural biology investigations). Accurate mass determination allows one to evaluate the correctness of protein primary sequences, the presence of mutations and/or post-translational modifications, the possible protein degradation, the sample homogeneity, and the degree of isotope incorporation in case of labelling (e.g.¹³C labelling).

Electrospray ionisation (ESI) mass spectrometry (MS) is widely used for mass determination of denatured proteins, but its efficiency is affected by the composition of the sample buffer. In particular, the presence of salts, detergents, and contaminants severely undermines the effectiveness of protein analysis by ESI-MS. Matrix-assisted laser desorption/ionization (MALDI) MS is an attractive alternative, due to its salt tolerance and the simplicity of data acquisition and interpretation. Moreover, the mass determination of large heterogeneous proteins (bigger than 100 kDa) is easier by MALDI-MS due to the absence of overlapping high charge state distributions which are present in ESI spectra.

Here we present an accessible approach for analysing proteins larger than 100 kDa by MALDI-time of flight (TOF). We illustrate the advantages of using a mixture of two matrices (i.e. 2,5-dihydroxybenzoic acid and α-cyano-4-hydroxycinnamic acid) and the utility of the thin layer method as approach for sample deposition. We also discuss the critical role of the matrix and solvent purity, of the standards used for calibration, of the laser energy, and of the acquisition time. Overall, we provide information necessary to a novice for analysing intact proteins larger than 100 kDa by MALDI-MS.

Accessing the reproducibility and specificity of pepsin and other aspartic proteases

The aspartic protease pepsin is less specific than other endoproteinases. Because aspartic proteases like pepsin are active at low pH, they are utilized in hydrogen deuterium exchange mass spectrometry (HDX MS) experiments for digestion under hydrogen exchange quench conditions. We investigated the reproducibility, both qualitatively and quantitatively, of online and offline pepsin digestion to understand the compliment of reproducible pepsin fragments that can be expected during a typical pepsin digestion. The collection of reproducible peptides was identified from >30 replicate digestions of the same protein and it was found that the number of reproducible peptides produced during pepsin digestion becomes constant above 5-6 replicate digestions. We also investigated a new aspartic protease from the stomach of the rice field eel (Monopterus albus Zuiew) and compared digestion efficiency and specificity to porcine pepsin and aspergillopepsin. Unique cleavage specificity was found for rice field eel pepsin at arginine, asparagine, and glycine. Different peptides produced by the various proteases can enhance protein sequence coverage and improve the spatial resolution of HDX MS data. This article is part of a Special Issue entitled: Mass spectrometry in structural biology.

Pepsin immobilized on high-strength hybrid particles for continuous flow online digestion at 10,000 psi

Pepsin was immobilized on ethyl-bridged hybrid (BEH) particles, and digestion performance was evaluated in a completely online format, with the specific intent of using the particles for hydrogen-deuterium exchange mass spectrometry (HDX MS) experiments. Because the BEH particles are mechanically strong, they could withstand prolonged, continuous high-pressure at 10,000 psi. Online digestion was performed under isobaric conditions with continuous solvent flow, in contrast to other approaches where the pressure or flow is cycled. As expected, digestion efficiency at 10,000 psi was increased and reproducibly produced more peptic peptides versus digestion at 1000 psi. Prototype columns made with the BEH pepsin particles exhibited robust performance, and deuterium back-exchange was similar to that of other immobilized pepsin particles. These particles can be easily incorporated in existing HDX MS workflows to provide more peptide coverage in experiments where fast, efficient, and reproducible online pepsin digestion is desired.

Polymorphisms of COTL1 gene identified by proteomic approach and their association with autoimmune disorders

To select candidate genes, we attempted to comparative analysis of protein levels between rheumatoid arthritis (RA) patients and healthy controls by two-dimensional electrophoresis (2-DE) and matrix-assisted laser desorption ionization mass spectrometry (MALDI-TOF-MS). We identified 17 proteins that showed up- or down-regulated spots in RA patients. We found that coactosin-like1 (COTL1) were highly expressed in RA patients compared with healthy controls. We performed a case-control study to determine whether the COTL1 gene polymorphisms were associated with RA and systemic lupus erythematosus (SLE). The genotype frequency of c.-1124G>T and the allelic frequency of c.484G>A in RA patients, and the genotype frequency of c.484G>A in SLE patients were significantly different from healthy controls (P=0.009, 0.027, and 0.025, respectively). We also investigated the correlation with the levels of rheumatoid factor (RF) and anti-cyclic citrullinated peptide (CCP) antibody in RA patients, and anti-nuclear antibodies (ANA) in SLE patients. The c.484G>A polymorphism in RA patients has significant association with the levels of anti-CCP antibody (P=0.03). Our findings demonstrated that c.-1124G>T and c. 484G>A polymorphisms of the COTL1 gene might be associated with the genetic susceptibility of autoimmune disorders.

Spectroscopic detection and identification of infected cells with herpes viruses

Matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) and Fourier transform infrared (FTIR) microspectroscopy were previously applied for the identification of various biological samples. In the present study, normal cells in culture and cells infected with herpes simplex virus type 2 (HSV-2) or varicella-zoster virus (VZV) were analyzed by MALDI-TOF and FTIR microscopy. Specific spectral biomarkers for rapid and reliable monitoring and identification of infected cells and probably for the discrimination between these viruses were searched. The results show consistent spectral peaks in all examined normal uninfected human fibroblast cells both in MALDI-T0F and FTIR microscopy. In HSV-2- or VZV-infected cells, two unique peaks for each appeared at m/z 5397 and 5813 or at m/z 3501 and 4951, respectively, in MALDI-TOF spectra. In addition, several peaks that appeared in control uninfected cells at the region m/z 13,000-20,000 disappeared completely in all examined infected samples. When these infected cells were examined by FTIR microscopy, a band at 859 cm(-1) in control uninfected cells was significantly shifted to 854 cm(-1) in both HSV2- and VZV-infected cells. In addition, phosphate levels were considerably increased in all infected cells compared to normal uninfected cells. These parameters could be used as a basis for developing a spectral method for the detection and identification of cells infected with herpes viruses.

Overview of the characterization of recombinant proteins

This overview provides guidelines for the characterization of recombinantly expressed proteins (e.g., verifying primary structure and appropriate post-translational modifications), along with methodologies for characterizing the proteins according to size, X-ray structure, absorbance, biological activity, and subunit structure. A flow chart presents a suggested path for fully characterizing recombinant protein and involves equipment for HPLC, mass spectrometry, circular dichroism, NMR and fluorescence spectroscopy. Also covered are sources and consequences of contamination in protein solutions.

Epitope mapping on bovine prion protein using chemical cross-linking and mass spectrometry

An analytical strategy for the analysis of antigen epitopes by chemical cross-linking and mass spectrometry is demonstrated. The information of antigen peptides involved in the binding to an antibody can be obtained by monitoring the antigen peptides modified by a partially hydrolyzed cross-linker in the absence and in the presence of an antibody. This approach was shown to be efficient for characterization of the epitope on bovine prion protein bPrP(25-241) specifically recognized by a monoclonal antibody, 3E7 (mAb3E7), with only a small amount of sample (200 picomoles) needed. After cross-linking of the specific immuno complex, a matrix-assisted laser desorption/ionization (MALDI) mass spectrometer equipped with an ion conversion dynode (ICD) high-mass detector was used to optimize the amount of cross-linked complex formed at 202 kDa before proteolytic digestion. To identify the cross-linked peptides after proteolysis without ambiguity, isotope-labeled cross-linkers, disuccinimidyl suberate (DSS-d0/d12) and disuccinimidyl glutarate (DSG-d0/d6), together with high-resolution Fourier transform ion-cyclotron resonance mass spectrometry (FTICR-MS) were used. As a result, a complete fading of the peak intensities corresponding to the peptides representing the epitope was observed when bPrP/mAb3E7 complexes were formed.

Analyzing RNA-protein crosslinking sites in unlabeled ribonucleoprotein complexes by mass spectrometry

Mass spectrometry is a powerful tool for the analysis of biomolecules, proteins, nucleic acids, carbohydrates, lipids. In combination with genome sequences that are available in the databases, it has proven to be the most straightforward and sensitive technique for the sequence analysis and hence the identification of protein components in the cells, their (post)translational modifications, and their relative and absolute abundance. In addition, mass spectrometric methods are successfully applied for the structural analysis of biomolecules (i.e., deciphering molecule-ligand interactions and spatial quartenary arrangements of molecule complexes). We describe a methodology for the mass spectrometric analysis of protein-RNA contact sites in purified ribonucleoprotein (RNP) particles. The method comprises ultraviolet (UV) crosslinking of proteins to RNA, hydrolysis of the protein and RNA moieties, isolation of cross-linked peptide-RNA oligonucleotides, MALDI (matrix-assisted laser desorption/ionization) mass spectrometry of the isolated conjugates to determine the sequence of the crosslinked peptide and RNA part. The utility of this methodology is demonstrated on crosslinks isolated from UV-irradiated spliceosomal particles; these were [15.5 K-61 K-U4atac] small nuclear ribonucleoprotein (snRNP) particles prepared by reconstitution in vitro and U1 snRNP particles purified from HeLa cells.

Fidelity of the protein structure reconstruction from inter-residue proximity constraints

Inter-residue proximity constraints obtained in such experiments as cross-linking/mass spectrometry are important sources of information for protein structure determination. A central question in structure determination using these constraints is, What is the minimal number of inter-residue constraints needed to determine the fold of a protein? It is also unknown how the different structural aspects of constraints differentiate their ability in determining the native fold and whether there is a rational strategy for selecting constraints that feature higher fidelity in structure determination. To shed light on these questions, we study the fidelity of protein fold determination using theoretical inter-residue proximity constraints derived from protein native structures and the effect of various subsets of such constraints on fold determination. We show that approximately 70% randomly selected constraints are sufficient for determining the fold of a domain (with an average root-mean-square deviation of <or=3.4 A from their native structures). We find that random constraint selection often outperforms the rational strategy that predominantly favors the constraints representing global structural features. To uncover a strategy for constraint selection for the optimal structure determination, we study the role of the topological properties of these constraints. Interestingly, we do not observe any correlation between various simple topological properties of the selected constraints, emphasizing different global and local structural features, and the performance of these constraints, suggesting that accurate protein structure determination relies on a composite of global and local structural information.

Material-enhanced laser desorption/ionization (MELDI)--a new protein profiling tool utilizing specific carrier materials for time of flight mass spectrometric analysis

Over the past couple of years, proteomics pattern analysis has emerged as an effective method for the early diagnosis of diseases such as ovarian, breast, or prostate cancer, without identification of single biomarkers. MALDI-TOF MS, for example, offers a simple approach for fast and reliable protein profiling, especially by using carrier materials with various physical and chemical properties, in combination with a MALDI matrix. This approach is referred to as material-enhanced laser desorption/ionization (MELDI). In this paper, we report the development and application of derivatized carrier materials [cellulose, silica, poly(glycidyl methacrylate/divinylbenzene) (GMA/DVB) particles, and diamond powder] for fast and direct MALDI-TOF MS protein profiling. The applicability of MELDI for rapid protein profiling was evaluated with human serum samples. These carriers, having various hydrophobicities, resulted in characteristic mass fingerprints, even if all materials were derivatized with iminodiacetic acid (IDA) to yield an immobilized metal affinity chromatography (IMAC) functionality. Our study demonstrates that analyzing complex biological samples, such as human serum, by employing different MELDI carrier materials yielded type- and size-dependent performance variation.

Chemical cross-linking and mass spectrometry for mapping three-dimensional structures of proteins and protein complexes

Chemical cross-linking of proteins, an established method in protein chemistry, has gained renewed interest in combination with mass spectrometric analysis of the reaction products for elucidating low-resolution three-dimensional protein structures and interacting sequences in protein complexes. The identification of the large number of cross-linking sites from the complex mixtures generated by chemical cross-linking, however, remains a challenging task. This review describes the most popular cross-linking reagents for protein structure analysis and gives an overview of the strategies employing intra- or intermolecular chemical cross-linking and mass spectrometry. The various approaches described in the literature to facilitate detection of cross-linking products and also computer software for data analysis are reviewed. Cross-linking techniques combined with mass spectrometry and bioinformatic methods have the potential to provide the basis for an efficient structural characterization of proteins and protein complexes.

Monitoring of unfolding of metallo-proteins by electrospray ionization mass spectrometry

An electrospray ionisation (ESI) mass spectrometric method for the determination of the equilibrium constant and free energy (DeltaG) of protein unfolding was used to monitor the denaturation process at different pH of three metallo-proteins, i.e. wild-type copper azurin, zinc azurin and wild-type amicyanin. The time course of the unfolding process was followed by dissolving the proteins under denaturing conditions (methanol-water (1 : 1, v/v)) at different pH (2.5, 3.0, 3.5) and recording ESI spectra at time intervals. The spectra showed two series of peaks, corresponding to the native holo-protein and the unfolded apo-protein. From the intensity ratio of these two series of peaks at increasing time and at equilibrium, the equilibrium constants for the unfolding process for the three proteins could be determined. From these equilibrium constants a DeltaG degrees derivation was attempted. The DeltaG degrees values obtained decrease with decrease in pH, in agreement with the expected reduction of conformational stability of proteins at lower pH. The results obtained confirm that ESI-MS can be used for monitoring of unfolding process and to derive quantitative thermodynamic data.

Sample preparation effects in matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry of partially depolymerised carboxymethyl cellulose

Sample preparation effects in matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOFMS) of partially depolymerised carboxymethyl cellulose (CMC) have been investigated. The depolymerisation was either enzymatic or acidic. Fractions of enzymatically depolymerised CMC were collected from size-exclusion chromatography (SEC) and further investigated by MALDI-TOFMS. 2,5-Dihydroxybenzoic acid was used as matrix, dissolved in H(2)O due to the poor solubility of CMC in suitable organic solvents. The samples were dried by two methods, in ambient atmosphere and at reduced pressure. Under reduced pressure the sample spot homogeneity increased. This drying method, however, produced additional adduct peaks in the mass spectra originating from ion exchange on the CMC oligomers. Analysis of CMC could be performed in both negative and positive ion modes. Mass discrimination and variation in ionisation efficiency were demonstrated by comparing mass spectra with SEC data. Measurements of the degree of substitution (DS) were performed on three CMCs with different DS values, which were depolymerised in trifluoroacetic acid. The three CMCs were easily distinguished from one another, but the obtained DS values deviated from the values supplied by the manufacturer.

Mapping low-resolution three-dimensional protein structures using chemical cross-linking and Fourier transform ion-cyclotron resonance mass spectrometry

Techniques in mass spectrometry (MS) combined with chemical cross-linking have proven to be efficient tools for the rapid determination of low-resolution three-dimensional (3-D) structures of proteins. The general procedure involves chemical cross-linking of a protein followed by enzymatic digestion and MS analysis of the resulting peptide mixture. These experiments are generally fast and do not require large quantities of protein. However, the large number of peptide species created from the digestion of cross-linked proteins makes it difficult to identify relevant intermolecular cross-linked peptides from MS data. We present a method for mapping low-resolution 3-D protein structures by combining chemical cross-linking with high-resolution FTICR (Fourier transform ion-cyclotron resonance) mass spectrometry using cytochrome c and hen egg lysozyme as model proteins. We applied several homo-bifunctional, amine-reactive cross-linking reagents that bridge distances from 6 to 16 A. The non-digested cross-linking reaction mixtures were monitored by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) to determine the extent of cross-linking. Enzymatically digested reaction mixtures were separated by nano-high-performance liquid chromatography (nano-HPLC) on reverse-phase columns applying water/acetonitrile gradients with flow rates of 200 nL/min. The nano-HPLC system was directly coupled to an FTICR mass spectrometer equipped with a nano-ESI (electrospray ionization) source. Cross-linking products were identified using a combination of the GPMAW software and ExPASy Proteomics tools. For correct assignment of the cross-linking products the key factor is to rely on a mass spectrometric method providing both high resolution and high mass accuracy, such as FTICRMS. By combining chemical cross-linking with FTICRMS we were able to rapidly define several intramolecular constraints for cytochrome c and lysozyme.

Monitoring the expression and purification of recombinant proteins by MALDI-TOF mass spectrometry

1Samples coming from biologic sources usually contain several contaminants that interfere seriously with Mass Spectrometry (MS) measurements. In this paper we report the application of MALDI-TOF MS to monitor recombinant protein expression and purification. The technique is based on the use of a C18 resin to clean and concentrate proteins in batch. The utility of this method is demonstrated for samples coming from different bacterial cultures expressing secreted and intracellular proteins ranging from 4 to 53 kDa. MALDI-TOF MS of peptide and proteins can be accomplished directly from complex bacterial cultures or from any purification step in a few minutes using the conventional stainless steel sample targets, allowing for a nearly instantaneous monitoring of the nature and integrity of recombinant expression products.

A solid sample preparation method that reduces signal suppression effects in the MALDI analysis of peptides

Here we report on the application of a solid-solid (SS) sample preparation protocol for the MALDI analysis of peptides and multicomponent peptide mixtures. Our results with a series of model peptides indicate that a SS MALDI sample preparation protocol is useful for the analysis of peptides in the 1-3 kDa mass range. MALDI mass spectra recorded for peptides in this size range using a SS sample preparation were of a quality comparable to spectra recorded using a conventional dried-droplet (DD) sample preparation. Our results with several model peptide mixtures indicate that one advantage of a SS sample preparation protocol for the MALDI analysis of peptides is that it can significantly reduce signal suppression effects in multicomponent mixtures. MALDI results obtained using a SS sample preparation protocol are also more reproducible than results obtained using a conventional DD sample preparation protocol.

Free energy for blue copper protein unfolding determined by electrospray ionisation mass spectrometry

An electrospray ionisation (ESI) mass spectrometric method for the determination of the free energy (DeltaG) of unfolding of proteins is described. The method was tested using three blue copper proteins: wild type azurin, Cys-3Ala/Cys-26Ala (C3A/C26A) azurin mutant and wild-type amicyanin. The time course of the denaturation process of the proteins dissolved in methanol/water (50:50, v/v, pH 3.5) was followed by recording ESI mass spectra at time intervals. The spectra showed two series of peaks, corresponding to the native holo-protein and the unfolded apo-protein. From the intensity ratio of these two series of peaks at increasing time and at equilibrium, the free energy for the unfolding process for the three proteins could be determined. To evaluate the reliability of the thermodynamic data obtained by the ESI mass spectrometric approach, the denaturation process was followed by UV-VIS spectroscopy. The two sets of data obtained by these independent methods were in good agreement indicating that the ESI-MS approach can be used to obtain reliable quantitative information about the protein unfolding process. In principle, this approach can be applied to other proteins and requires very low amounts of sample, due to the intrinsic sensitivity of mass spectrometry. This may prove particularly useful when the amount of sample available prevents the use of current methods.

Monitoring of immune response by blood serum profiling using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

The application of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) to the analysis of blood serum leads to the observation of a large variety of reproducible mass spectral peaks corresponding to blood components. In this study, the use of MALDI-TOFMS was developed as a tool for monitoring immune response to bacterial infection. Employing the MALDI-TOFMS approach, the levels of many components of blood were found to be immune response independent whereas others were found to correlate directly with the response of the immune system to two known types of bacteria (Staphylococcus aureus and Enterococcus faecalis). The methodologies reported here should be useful for the rapid monitoring of blood, especially that of the immune response mechanisms in various animal species.

High throughput protein fold identification by using experimental constraints derived from intramolecular cross-links and mass spectrometry

We have used intramolecular cross-linking, MS, and sequence threading to rapidly identify the fold of a model protein, bovine basic fibroblast growth factor (FGF)-2. Its tertiary structure was probed with a lysine-specific cross-linking agent, bis(sulfosuccinimidyl) suberate (BS(3)). Sites of cross-linking were determined by tryptic peptide mapping by using time-of-flight MS. Eighteen unique intramolecular lysine (Lys-Lys) cross-links were identified. The assignments for eight cross-linked peptides were confirmed by using post source decay MS. The interatomic distance constraints were all consistent with the tertiary structure of FGF-2. These relatively few constraints, in conjunction with threading, correctly identified FGF-2 as a member of the beta-trefoil fold family. To further demonstrate utility, we used the top-scoring homolog, IL-1beta, to build an FGF-2 homology model with a backbone error of 4.8 A (rms deviation). This method is fast, is general, uses small amounts of material, and is amenable to automation.

On-probe solid-phase extraction/MALDI-MS using ion-pairing interactions for the cleanup of peptides and proteins

Samples originating from biological sources often contain a complex mixture of inorganic salts, buffers, chaotropic agents, surfactants/detergents, preservatives, and other solubilizing agents. However, the presence of these contaminants virtually ensures the failure of any subsequent analysis of the sample by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). Sample cleanup procedures, therefore, must be performed prior to MALDI-MS analysis. This paper reports a probe-surface derivatization method that greatly simplifies this sample preparation process. MALDI probes possessing self-assembled monolayers (SAMs) terminated with ionic functional groups can rapidly extract peptides/proteins via ionic interactions from < or = 1-microL volumes of sample solutions placed directly on their surface. We have found that MALDI probes modified in this manner are a practical solution for analyzing very small volumes of peptide/protein solutions contaminated with high levels of inorganic salts, buffers, detergents, chaotropic agents, and other solubilizing agents.

A desalting approach for MALDI-MS using on-probe hydrophobic self-assembled monolayers

One of the problems encountered in preparing samples for matrix-assisted laser desorption/ionization (MALDI) analysis is the presence of nonvolatile salts in the sample. This difficulty is often exacerbated by the necessity to prepare the sample in the appropriate sample-to-matrix ratio. This paper reports a probe surface derivatization method that greatly simplifies this sample preparation process. By constructing self-assembled monolayers of octadecyl mercaptan (C18) on the MALDI probe surface, we were able to generate a surface capable of reversibly binding polypeptides via hydrophobic interactions, which in turn, permits the analyte to be easily concentrated and desalted directly on the probe tip.

Mass spectrometry as a readout of protein structure and function

Proteins have evolved to carry out very specific functions within the cell by interacting with a diverse set of biomolecules. Understanding how a protein's higher order structure relates to its function is important for defining the molecular basis of these interactions. In recent years, mass spectrometry has become an important tool for dissecting protein structure and function. Using electrospray ionization (ESI)- and matrix-assisted laser desorption/ionization (MALDI)-based approaches, it has been possible to monitor protein folding, characterize noncovalent protein complexes, and assess the contribution of individual amino acid residues to a protein's function. Here, it is our goal to summarize these approaches and highlight recent, biologically relevant applications where mass spectrometry has provided unique insight into the mysteries of protein structure and function.

Efficient peptide ladder sequencing by MALDI-TOF mass spectrometry using allyl isothiocyanate

A new modification of the peptide ladder sequencing technique is described in which allyl isothiocyanate (AITC) replaces trifluoroethyl isothiocyanate as the volatile amine-modification reagent. AITC is commercially available, readily purified, stable up to 80 degrees C and reacts cleanly and rapidly with all amino groups of polypeptides. Several model peptides and two side chain-modified peptides were sequentially degraded using AITC and the cleavage reagent heptafluorobutyric acid (HFBA) up to seven amino acids from the N-terminus. Matrix-assisted laser-desorption and ionization coupled with time-of-flight (MALDI-TOF) mass spectroscopy of the peptide mixture provided a clear ladder-like mass profile with consecutive molecular ions corresponding to each shortened peptide at picomole range. The results indicate the general utility of this analytical protocol by the use of AITC as the amine-coupling reagent.

Mass spectrometry in protein studies from genome to function

The demands for highly sensitive and specific analytical techniques in biochemistry, molecular biology and biotechnology are met by new developments in mass spectrometry. Femto- to attomole sensitivity and mass accuracy in a low parts per million range can now be routinely obtained. Mass spectrometry, already accepted for studies of protein secondary modifications, must, in the future, be expected to be an important tool in protein studies on all levels, ranging from proteome analysis to studies of protein higher order structures and protein interaction.

Monitoring proteolysis of recombinant human interferon-gamma during batch culture of Chinese hamster ovary cells

Proteolytic cleavage of recombinant human interferon-gamma (IFN-gamma) expressed in Chinese hamster ovary (CHO) cells during batch fermentation has been monitored by mass spectrometric peptide mapping. IFN-gamma was purified from cell-free culture supernatant by immunoaffinity chromatography and cleaved by endoprotease Asp-N. Peptide fragments were resolved by reverse-phase HPLC and identified by a combination of matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) and automated N-terminal peptide sequencing. Using this approach, a peptide was identified as the C-terminal fragment of the IFN-gamma polypeptide. Analysis of this peptide by MS indicated that the recombinant IFN-gamma polypeptide secreted by CHO cells was truncated by at least ten amino acids, initially at Gln133-Met134. No full length (143 amino acids) polypeptide molecules were observed at any stages of the fermentation. Additional proteolytic cleavages at basic amino acids N-terminal of Gln133 occurred during the later stages of the culture resulting in a heterogeneous IFN-gamma polypeptide with "ragged" C-termini.

Characterization of peptide-oligonucleotide heteroconjugates by mass spectrometry

Two peptide-oligothymidylic acids, prepared by joining an 11 residue synthetic peptide containing one internal carboxyl group (Asp side chain) to amino-linker-5'pdT6 and amino-linker-5'pdT10 oligonucleotides, were analyzed by matrix-assisted laser desorption/ionization (MALDI) on a linear time-of-flight mass spectrometer and by electrospray ionization (ESI) on a triple-quadrupole system. These synthetic compounds model peptide-nucleic acid heteroconjugates encountered in antisense research and in studies that use photochemical crosslinking to investigate molecular aspects of protein-nucleic acid interactions. MALDI and ESI sensitivities for the two hybrid compounds were found to be similar respectively to their sensitivities for the pure oligonucleotide parts. In general, MALDI proved to be less affected by sample impurities and more sensitive than ESI, while ESI on the quadrupole produced greater mass accuracy and resolution than MALDI on the time-of-flight instrument. A hybrid's behavior in a MALDI-matrix or an ESI-spray-solvent was found to be governed mainly by the oligonucleotide. A single positive ESI tandem mass spectrum of the peptide-dT6 accounted for the heteroconjugate's entire primary structure including the point of the oligonucleotide's covalent attachment to the peptide.

Posttranslational processing of recombinant human interferon-gamma in animal expression systems

We have characterized the heterogeneity of recombinant human interferon-gamma (IFN-gamma) produced by three expression systems: Chinese hamster ovary cells, the mammary gland of transgenic mice, and baculovirus-infected Spodopera frugiperda (Sf9) insect cells. Analyses of whole IFN-gamma proteins by electrospray ionization-mass spectrometry (ESI-MS) from each recombinant source revealed heterogeneous populations of IFN-gamma molecules resulting from variations in N-glycosylation and C-terminal polypeptide cleavages. A series of more specific analyses assisted interpretation of maximum entropy deconvoluted ESI-mass spectra of whole IFN-gamma proteins; MALDI-MS analyses of released, desialylated N-glycans and of deglycosylated IFN-gamma polypeptides were combined with analyses of 2-aminobenzamide labeled sialylated N-glycans by cation-exchange high-performance liquid chromatography. These analyses enabled identification of specific polypeptide cleavage sites and characterization of associated N-glycans. Production of recombinant IFN-gamma in the mammalian expression systems yielded polypeptides C-terminally truncated at dibasic amino acid sites. Mammalian cell derived IFN-gamma molecules displayed oligosaccharides with monosaccharide compositions equivalent to complex, sialylated, or high-mannose type N-glycans. In contrast, IFN-gamma derived from baculovirus-infected Sf9 insect cells was truncated further toward the C-terminus and was associated with neutral (nonsialylated) N-glycans. These data demonstrate the profound influence of host cell type on posttranslational processing of recombinant proteins produced in eukaryotic systems.

Developments in matrix-assisted laser desorption/ionization peptide mass spectrometry

Most characteristics of matrix-assisted laser desorption/ionization (MALDI) are ideal for the analysis of biomolecules. New preparation techniques have dramatically increased mass accuracy and resolution, making MALDI a high-performance mass spectrometric technique for peptide mass analysis. Attempts to obtain amino acid sequence information by MALDI have been partially successful. The technique has been put to novel uses in protein primary structure characterization.

Sequence verification of human creatine kinase (43 kDa) isozymes by high-resolution tandem mass spectrometry

Amino acid sequencing by recombinant DNA technology, although dramatically useful, is subject to base reading errors, is indirect, and is insensitive to posttranslational processing. Mass spectrometry techniques can provide molecular weight data from even relatively large proteins for such cDNA sequences and can serve as a check of an enzyme's purity and sequence integrity. Multiply-charged ions from electrospray ionization can be dissociated to yield structural information by tandem mass spectrometry, providing a second method for gaining additional confidence in primary sequence confirmation. Here, accurate (+/- 1 Da) molecular weight and molecular ion dissociation information for human muscle and brain creatine kinases has been obtained by electrospray ionization coupled with Fourier-transform mass spectrometry to help distinguish which of several published amino acid sequences for both enzymes are correct. The results herein are consistent with one published sequence for each isozyme, and the heterogeneity indicated by isoelectric focusing due to 1-Da deamidation changes. This approach appears generally useful for detailed sequence verification of recombinant proteins.

Ezrin oligomers are major cytoskeletal components of placental microvilli: a proposal for their involvement in cortical morphogenesis

Ezrin is a component of the microvillus cytoskeleton of a variety of polarized epithelial cells and is believed to function as a membrane-cytoskeletal linker. In this study, we isolated microvilli from human placental syncytiotrophoblast as a model system for biochemical analysis of ezrin function. In contrast to intestinal microvilli, ezrin is a major protein component of placental microvilli, comprising approximately 5% of the total protein mass and present at about one quarter of the molar abundance of actin. Gel filtration and chemical cross-linking studies demonstrated that ezrin exists mainly in the form of noncovalent dimers and higher order oligomers in extracts of placental microvilli. A novel form of ezrin, apparently representing covalently cross-linked adducts, was present as a relatively minor constituent of placental microvilli. Both oligomers and adducts remained associated with the detergent-insoluble cytoskeleton, indicating a tight interaction with actin filaments. Moreover, stimulation of human A431 carcinoma cells with EGF induces the rapid formation of ezrin oligomers in vivo, thus identifying a signal transduction pathway involving ezrin oligomerization coincident with microvillus assembly. In addition to time course studies, experiments with tyrosine kinase and tyrosine phosphatase inhibitors revealed a correlation between the phosphorylation of ezrin on tyrosine and the onset of oligomer formation, consistent with the possibility that phosphorylation of ezrin might be required for the generation of stable oligomers. Based on these observations, a model for the assembly of cell surface structures is proposed.

Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS)

Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) has been responsible for solving many problems in structural biology. Mass analysis is now used routinely to confirm proper expression and processing of proteins, and to locate and identify post-translational modifications. Innovative advances in instrumentation have led to higher mass resolution and mass accuracy. New sample preparation methods are likewise yielding higher sensitivity plus greater tolerance for buffer components that have in the past suppressed signals at higher concentrations. Advancements in the technique have also led to new or improved applications in many areas, including peptide sequencing and the identification of proteins by database searching with peptide masses. Instruments with lower cost, smaller size, and higher performance are making mass measurements available to an increasing number of laboratories. MALDI-MS is poised to continue to improve in performance and in its usefulness for current and new applications.

Probing the solution structure of the DNA-binding protein Max by a combination of proteolysis and mass spectrometry

A simple biochemical method that combines enzymatic proteolysis and matrix-assisted laser desorption ionization mass spectrometry was developed to probe the solution structure of DNA-binding proteins. The method is based on inferring structural information from determinations of protection against enzymatic proteolysis, as governed by solvent accessibility and protein flexibility. This approach was applied to the study of the transcription factor Max--a member of the basic/helix-loop-helix/zipper family of DNA-binding proteins. In the absence of DNA and at low ionic strengths, Max is rapidly digested by each of six endoproteases selected for the study, results consistent with an open and flexible structure of the protein. At physiological salt levels, the rates of digestion are moderately slowed; this and the patterns of cleavage are consistent with homodimerization of the protein through a predominantly hydrophobic interface. In the presence of Max-specific DNA, the protein becomes dramatically protected against proteolysis, exhibiting up to a 100-fold reduction in cleavage rates. Over a 2-day period, both complete and partial proteolysis of the Max-DNA complex is observed. The partial proteolytic fragmentation patterns reflect a very high degree of protection in the N-terminal and helix-loop-helix regions of the protein, correlating with those expected of a stable dimer bound to DNA at its basic N-terminals. Less protection is seen at the C-terminal where a slow, sequential proteolytic cleavage occurs, correlating to the presence of a leucine zipper. The results also indicate a high affinity of Max for its target DNA that remains high even when the leucine zipper is proteolytically removed. In addition to the study of the helix-loop-helix protein Max, the present method appears well suited for a range of other structural biological applications.

Increased stability of nucleic acids containing 7-deaza-guanosine and 7-deaza-adenosine may enable rapid DNA sequencing by matrix-assisted laser desorption mass spectrometry

The use of matrix-assisted laser desorption mass spectrometry (MALDI-MS) has been suggested as an ultrafast readout of Sanger DNA sequencing ladders in a manner analogous to that used with sequencing gels. Currently, a serious limitation of MALDI-MS for the analysis of DNA results from the tendency for oligonucleotides to undergo facile fragmentation in the gas phase. The present study was undertaken to gain an understanding of the influence of various chemical structural features of purine bases on the stability of oligodeoxynucleotide ions produced by MALDI. The study focused on the stability of model compounds of the type d(TTTTTTTTTTXTTTTTTTTT TTTT), where T designates deoxythymidine and X a purine-containing 2'-deoxynucleotide. A variety of different purine derivatives were chosen as the base in the nucleotide X. The mass spectra of the model compounds containing 7-deaza analogues of guanine and adenine reveal a significantly increased stability compared to the 7-aza analogues under the conditions of MALDI-MS. The previously reported incorporation of the 7-deaza-2'-deoxy-adenosine triphosphate and the 7-deaza-2'-deoxy-guanosine triphosphate into DNA by polymerases suggests their use in a Sanger dideoxy sequencing experiment. The dideoxy termination products with the 7-deaza-purines instead of the 7-aza-purines might be sufficiently stable to allow separation and detection of the sequencing ladder by MALDI-MS. Thus, an ultrafast (seconds) read-out of DNA sequence may become feasible.

Tropomyosin is essential in yeast, yet the TPM1 and TPM2 products perform distinct functions

Sequence analysis of chromosome IX of Saccharomyces cerevisiae revealed an open reading frame of 166 residues, designated TPM2, having 64.5% sequence identity to TPM1, that encodes the major form of tropomyosin in yeast. Purification and characterization of Tpm2p revealed a protein with the characteristics of a bona fide tropomyosin; it is present in vivo at about one sixth the abundance of Tpm1p. Biochemical and sequence analysis indicates that Tpm2p spans four actin monomers along a filament, whereas Tpmlp spans five. Despite its shorter length, Tpm2p can compete with Tpm1p for binding to F-actin. Over-expression of Tpm2p in vivo alters the axial budding of haploids to a bipolar pattern, and this can be partially suppressed by co-over-expression of Tpm1p. This suggests distinct functions for the two tropomyosins, and indicates that the ratio between them is important for correct morphogenesis. Loss of Tpm2p has no detectable phenotype in otherwise wild type cells, but is lethal in combination with tpm1 delta. Over-expression of Tpm2p does not suppress the growth or cell surface targeting defects associated with tpm1 delta, so the two tropomyosins must perform an essential function, yet are not functionally interchangeable. S. cerevisiae therefore provides a simple system for the study of two tropomyosins having distinct yet overlapping functions.