Elemental mass spectrometry for quantitative proteomics

In the last decade mass-spectrometry-based proteomics has become an indispensable analytical tool for molecular biology, cellular biology and, lately, for the emerging systems biology. This review summarises the evolution and great potential of analytical methods based on elemental mass-spectrometric detection for quantitative proteomic analysis.     

Analysis of protein interaction networks using mass spectrometry compatible techniques

The ability to map protein-protein interactions has grown tremendously over the last few years, making it possible to envision the mapping of whole or targeted protein interaction networks and to elucidate their temporal dynamics. The use of mass spectrometry for the study of protein complexes has proven to be an invaluable tool due to its ability to unambiguously identify proteins from a variety of biological samples. Furthermore, when affinity purification is combined with mass spectrometry analysis, the identification of multimeric protein complexes is greatly facilitated. Here, we review recent developments for the analysis of protein interaction networks by mass spectrometry and discuss the integration of different bioinformatic tools for predicting, validating, and managing interaction datasets.     

Interpretation of mass spectrometry data for high-throughput proteomics

Recent developments in proteomics have revealed a bottleneck in bioinformatics: high-quality interpretation of acquired MS data. The ability to generate thousands of MS spectra per day, and the demand for this, makes manual methods inadequate for analysis and underlines the need to transfer the advanced capabilities of an expert human user into sophisticated MS interpretation algorithms. The identification rate in current high-throughput proteomics studies is not only a matter of instrumentation. We present software for high-throughput PMF identification, which enables robust and confident protein identification at higher rates. This has been achieved by automated calibration, peak rejection, and use of a meta search approach which employs various PMF search engines. The automatic calibration consists of a dynamic, spectral information-dependent algorithm, which combines various known calibration methods and iteratively establishes an optimised calibration. The peak rejection algorithm filters signals that are unrelated to the analysed protein by use of automatically generated and dataset-dependent exclusion lists. In the "meta search" several known PMF search engines are triggered and their results are merged by use of a meta score. The significance of the meta score was assessed by simulation of PMF identification with 10,000 artificial spectra resembling a data situation close to the measured dataset. By means of this simulation the meta score is linked to expectation values as a statistical measure. The presented software is part of the proteome database ProteinScape which links the information derived from MS data to other relevant proteomics data. We demonstrate the performance of the presented system with MS data from 1891 PMF spectra. As a result of automatic calibration and peak rejection the identification rate increased from 6% to 44%.Abbreviations 2-DE Two-dimensional gel electrophoresis - MALDI Matrix-assisted laser desorption ionisation - PMF Peptide mass fingerprinting - MS Mass spectrometry - TOF Time of flight     

Ion mobility–mass spectrometry: a new paradigm for proteomics

Matrix-assisted laser desorption/ionization (MALDI) coupled with ion mobility–mass spectrometry (IM–MS) provides a rapid (μs–ms) means for the two-dimensional (2D) separation of complex biological samples (e.g., peptides, oligonucleotides, glycoconjugates, lipids, etc.), elucidation of solvent-free secondary structural elements (e.g., helices, β-hairpins, random coils, etc.), rapid identification of post-translational modifications (e.g., phosphorylation, glycosylation, etc.) or ligation of small molecules, and simultaneous and comprehensive sequencing information of biopolymers. In IM–MS, protein-identification information is complemented by structural characterization data, which is difficult to obtain using conventional proteomic techniques. New avenues for enhancing the figures of merit (e.g., sensitivity, limits of detection, dynamic range, and analyte selectivity) and optimizing IM–MS experimental parameters are described in the context of deriving new information at the forefront of proteomics research.     

A pyrolysis mass spectrometry study of polythiophene copolymers

The thermal behaviour of copolymers of thiophene with decanedioic acid bis-(2-thiophen-3-yl-ethyl)ester (DATE) and terephthalic acid bis-(2-thiophen-3-yl-ethyl)ester (TATE) prepared by potentiostatic polymerization was studied via pyrolysis mass spectrometry. It was determined that the electrolytic films correspond to the related homopolymers. The increase in thermal stability of ester linkages, and evolution of characteristic degradation products of TATE and DATE together with thiophene based products above 400 °C confirmed copolymer formation.     

Verification of protein biomarker specificity for the identification of biological stains by quadrupole time‐of‐flight mass spectrometry

Advances in proteomics technology over the past decade offer forensic serologists a greatly improved opportunity to accurately characterize the tissue source from which a DNA profile has been developed. Such information can provide critical context to evidence and can help to prioritize downstream DNA analyses. Previous proteome studies compiled panels of “candidate biomarkers” specific to each of five body fluids (i.e ., peripheral blood, vaginal/menstrual fluid, seminal fluid, urine, and saliva). Here, a multiplex quadrupole time‐of‐flight mass spectrometry assay has been developed in order to verify the tissue/body fluid specificity the 23 protein biomarkers that comprise these panels and the consistency with which they can be detected across a sample population of 50 humans. Single‐source samples of these human body fluids were accurately identified by the detection of one or more high‐specificity biomarkers. Recovery of body fluid samples from a variety of substrates did not impede accurate characterization and, of the potential inhibitors assayed, only chewing tobacco juice appeared to preclude the identification of a target body fluid. Using a series of 2‐component mixtures of human body fluids, the multiplex assay accurately identified both components in a single‐pass. Only in the case of saliva and peripheral blood did matrix effects appear to impede the detection of salivary proteins.     

Pyridinium-based ionic liquid matrices can improve the identification of proteins by peptide mass-fingerprint analysis with matrix-assisted laser desorption/ionization mass spectrometry

Matrix-assisted laser desorption/ionization mass spectrometry has become an indispensable tool for identification of proteins by peptide mass-fingerprint analysis. Selection of the matrix, addition of matrix additives, and sample-preparation techniques are known to affect the quality of the spectra and hence protein identification. We investigated the effect of pyridine as matrix additive for the commonly used crystalline matrix α-cyano-4-hydroxycinnamic acid (CCA), forming a pyridinium based ionic liquid matrix, on the mass spectra of synthetic peptides and tryptic protein digests. Beside the equimolar mixture of CCA and pyridine, the effect of addition of substoichiometric amounts of the base to the acid was tested. Optimum results in terms of signal-to-noise ratios, reduction of chemical noise, and reduced formation of alkali adducts and matrix clusters were observed for the matrix CCA–pyridine in the molar ratio 2:1. The optimized ionic liquid matrix was used for identification of tryptic digests of six model proteins and for identification of a protein extracted from a two-dimensional gel with the proteome of the bacterium Corynebacterium glutamicum, and shown to facilitate protein identification, yielding higher scores and increased sequence coverage compared with pure CCA. Thus CCA–Py 2:1 is a potential alternative for identification and characterization of proteins by peptide mass-fingerprint analysis. This paper was presented at the 38th Annual Meeting of the German Society for Mass Spectrometry (DGMS) held in March 2005 in Rostock, Germany.     

Technical innovations for the automated identification of gel-separated proteins by MALDI-TOF mass spectrometry

The combination of gel-based two-dimensional protein separations with protein identification by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) is the workhorse for the large-scale analyses of proteomes. Such high-throughput proteomic approaches require automation of all post-separation steps and the in-gel digest of proteins especially is often the bottleneck in the protein identification workflow. With the objective of reaching the same high performance of manual low-throughput in-gel digest procedures, we have developed a novel stack-type digestion device and implemented it into a commercially available robotic liquid handling system. This modified system is capable of performing in-gel digest, extraction of proteolytic peptides, and subsequent sample preparation for MALDI-MS without any manual intervention, but with a performance at least identical to manual procedures as indicated on the basis of the sequence coverage obtained by peptide mass fingerprinting. For further refinement of the automated protein identification workflow, we have also developed a motor-operated matrix application device to reproducibly obtain homogenous matrix preparation of high quality. This matrix preparation was found to be suitable for the automated acquisition of both peptide mass fingerprint and fragment ion spectra from the same sample spot, a prerequisite for high confidence protein identifications on the basis of peptide mass and sequence information. Due to the implementation of the stack-type digestion device and the motor-operated matrix application device, the entire platform works in a reliable, cost-effective, and sensitive manner, yielding high confidence protein identifications even for samples in the concentration range of as low as 100 fmol protein per gel plug.      

FluClass: A novel algorithm and approach to score and visualize the phylogeny of the influenza virus using mass spectrometry

A novel computer algorithm FluClass has been developed to facilitate the phylogenetic classification of influenza virus using mass spectral data. FluClass accepts a DNA or protein-based phylogenetic tree as input and generates theoretical peptide mass lists for each node. An experimental mass spectrum from an influenza virus protein digest is then placed onto the phylogenetic tree using a novel random resampling function (Z-score) that allows the scoring of spectrum against both internal and leaf nodes. Testing of the algorithm using hemagglutinin protein sequences from human-host influenza viruses showed that the Z-score performs comparably to the Profound scoring method for the scoring of leaf nodes and is substantially better at scoring internal nodes. Scoring of internal nodes allows colorizations of nodes of the phylogenetic tree enabling the classification of the query spectrum to be rapidly visualized. Finally we demonstrate the utility of FluClass on experimental spectra from six strains. Given that mass spectrometry data can be generated rapidly for influenza virus proteins, FluClass provides a fast and direct method for phylogenetic analysis of influenza proteins.     

Quantitative mass spectrometry in biochemistry and medicine.

The current state of quantitative analysis with the mass spectrometer in biochemistry and medicine is reviewed. The basic principles of mass spectrometry, the latter's combination with chromatography, the development of sensitive, exact, and in particular specific mass-spectrometric methods of detection, and the principle of dilution with stable isotopes are illustrated by examples. The most important fields of application are: the pharmacokinetics of drugs and active metabolites, investigation of metabolic pathways, supporting of medical diagnoses and enhancement of their specificity, and finally checking the quality of simpler quantitative processes in clinical chemistry.     

Evaluation of chemical labeling methods for identifying functional arginine residues of proteins by mass spectrometry

Arginine residues undergo several kinds of post-translational modifications (PTMs). These PTMs are associated with several inflammatory diseases, such as rheumatoid arthritis, atherosclerosis, and diabetes. Mass spectrometric studies of arginine modified proteins and peptides are very important, not only to identify the reactive arginine residues but also to understand the tandem mass spectrometry behavior of these peptides for assigning the sequences unambiguously. Herein, we utilize tandem mass spectrometry to report the performance of two widely used arginine labeling reagents, 1,2-cyclohexanedione (CHD) and phenylglyoxal (PG) with several arginine containing peptides and proteins. Time course labeling studies were performed to demonstrate the selectivity of the reagents in proteins or protein digests. Structural studies on the proteins were also explored to better understand the reaction sites and position of arginine residues. We found CHD showed better labeling efficiencies compared to phenylglyoxal. Reactive arginine profiling on a purified albumin protein clearly pointed out the cellular glycation modification site for this protein with high confidence.     

Automated sample preparation method for mass spectrometry analysis on recombinant proteins

A completely automated procedure for the purification and desalting of proteins with a polyhistidine purification tag prior to mass spectrometry analysis is presented. The system is ideal for rapid quality control and optimization studies and it provides researchers with a straightforward, reliable tool for studies of recombinant proteins. Forty-eight samples can be prepared within 4.5 h and only small cultivation and buffer volumes are needed. In this proof of concept, 19,000–35,000 Da recombinant proteins from both crude and clarified cell lysates were successfully prepared for subsequent analysis by electrospray ionization and matrix-assisted laser desorption/ionization mass spectrometry as well as by gel electrophoresis.     

Casein phosphoproteome: identification of phosphoproteins by combined mass spectrometry and two-dimensional gel electrophoresis

We report a fast and easy-to-use procedure that combines polyacrylamide gel electrophoresis with matrix assisted laser desorption/ionization-time of flight-mass spectrometry (MALDI-TOF) and nanoelectrospray-tandem mass spectrometry (nES-MS/MS) analysis for the identification of casein components and defined phosphorylated sites. This methodology ensured identification of more than 30 phosphorylated proteins, five beta-, fifteen alpha(s1)-, ten alpha(s2)-, and four kappa-casein (CN) components, including nonallelic, differently phosphorylated, and glycosylated forms. The sugar motif covalently bound to kappa-CN was identified as chains, trisaccharide GalNAc, Gal, NeuGc, and tetrasaccharide 1GalNAc, 1Gal, 2NeuGc. Also identified was a biantennary chain made up of both chains of trisaccharide 1GalNAc, 1Gal, 1NeuGc, and tetrasaccharide 1GalNAc, 1Gal, 2NeuGc moiety on a single kappa-CN component. The phosphate group on site Ser12 of tryptic peptide 8-22 of most phosphorylated alpha(s1)-CN (11 phosphate groups) was localized and the oligosaccharide sequence of the main tryptic glycopeptides of two kappa-CN components was determined by means of MS/MS analysis.     

A study of the applicability of various ionization methods and tandem mass spectrometry in the analyses of triphenyltin compounds

Triphenyltin compounds are widely introduced into the Dutch aquatic environment. To be able to detect them in environmental samples, the ionization methods of electron ionization, chemical ionization, fast atom bombardment, field desorption, thermospray and electrospray have been applied to triphenyltin acetate, chloride, fluoride and hydroxide to find out which of these methods is best suited to obtain molecular weight information on the intact molecules. For this purpose, field desorption is shown to be the most appropriate method giving, without fragmentation, molecular ion peaks, with the exception of triphenyltin hydroxide. The latter compound gives rise to the base peak at m/z 716, due to the formation of bis(triphenyltin)oxide. Field desorption tandem mass spectrometry, applied to the molecular ions, has shown that the main decomposition pathway corresponds to the loss of a phenyl radical. Subsequently, sediment and surface water samples from the Dutch inland water, without and with the use of clean-up procedures, have been analyzed by the application of field desorption in combination with tandem mass spectrometry. Within the limits of detection, no signals for the presence of triphenyltin compounds in these environmental samples has been found. Upon spiking these samples with triphenyltin acetate, chloride, fluoride and hydroxide, it has appeared that the covalently bonded non-aromatic substituent of the molecules is exchanged for hydroxyl.     

Analysis of food proteins and peptides by mass spectrometry-based techniques

Mass spectrometry has arguably become the core technology for the characterization of food proteins and peptides. The application of mass spectrometry-based techniques for the qualitative and quantitative analysis of the complex protein mixtures contained in most food preparations is playing a decisive role in the understanding of their nature, structure, functional properties and impact on human health. The application of mass spectrometry to protein analysis has been revolutionized in the recent years by the development of soft ionization techniques such as electrospray ionization and matrix assisted laser desorption/ionization, and by the introduction of multi-stage and ‘hybrid’ analyzers able to generate de novo amino acid sequence information. The interfacing of mass spectrometry with protein databases has resulted in entirely new possibilities of protein characterization, including the high sensitivity mapping (femtomole to attomole levels) of post-translational and other chemical modifications, protein conformations and protein–protein and protein–ligand interactions, and in general for proteomic studies, building up the core platform of modern proteomic science. MS-based strategies to food and nutrition proteomics are now capable to address a wide range of analytical questions which include issues related to food quality and safety, certification and traceability of (typical) products, and to the definition of the structure/function relationship of food proteins and peptides. These different aspects are necessarily interconnected and can be effectively understood and elucidated only by use of integrated, up-to-date analytical approaches. In this review, the main aspects of current and perspective applications of mass spectrometry and proteomic technologies to the structural characterization of food proteins are presented, with focus on issues related to their detection, identification, and quantification, relevant for their biochemical, technological and toxicological aspects.     

Nanomaterials in mass spectrometry ionization and prospects for biological application

The rapid development of nanotechnology has revolutionized scientific developments in recent decades. Mass spectrometry (MS) measurements are no exception and have benefited greatly from integration of nanomaterials in every step of analysis. This brief review summarizes recent developments in the field with the focus on the use of nanomaterials as alternative media to facilitate analyte ionization in laser-desorption ionization–mass spectrometry (LDI–MS) and secondary ion mass spectrometry (SIMS). The biological applications of both techniques are also detailed. The use of nanomaterials in other aspects of MS analysis, for example in sample clean-up and indirect analyte quantification, is briefly discussed.     

Enhanced mass resolution tandem mass spectrometry method for 2,3,7,8-tetrachlorodibenzo-p-dioxin detection with ion trap mass spectrometry using high damping gas pressure

Damping gas flow was optimized for 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) determination using ion trap mass spectrometer. A tandem mass spectrometry (MS-MS) method with better than unit-mass resolution (mass width, 0.3 u) was developed at a damping gas flow of 1.5 ml/min and a collision-induced dissociation (CID) voltage of 3.30 V. The relative standard deviation (R.S.D.) at the enhanced resolution was 2.9% in 24 h of consecutive injections. The detection limit was significantly improved because the efficiency of both precursor ion trapping and fragmentation increased with the damping gas flow. Product ion yield was 4.5 times higher and limit of detection was 3.2 times lower than at the default flow (0.3 ml/min and 1.65 V).     

Review of molecular modification techniques for improved detection of biomolecules by mass spectrometry

After a soft ionizing method was established, MS (mass spectrometry) has become a more common tool in biochemistry because soft ionization made it possible to detect large molecules such as proteins. Many kinds of applications were established to further utilize MS for the identification or quantitation of biomolecules. In this review, we introduce recent applications with special focus on chemical modification techniques and chemical probes developed for the MS determination of biomolecules.     

Discovery of safety biomarkers for atorvastatin in rat urine using mass spectrometry based metabolomics combined with global and targeted approach

In order to develop a safety biomarker for atorvastatin, this drug was orally administrated to hyperlipidemic rats, and a metabolomic study was performed. Atorvastatin was given in doses of either 70 mg kg⁻¹ day⁻¹ or 250 mg kg⁻¹ day⁻¹ for a period of 7 days (n = 4 for each group). To evaluate any abnormal effects of the drug, physiological and plasma biochemical parameters were measured and histopathological tests were carried out. Safety biomarkers were derived by comparing these parameters and using both global and targeted metabolic profiling. Global metabolic profiling was performed using liquid chromatography/time of flight/mass spectrometry (LC/TOF/MS) with multivariate data analysis. Several safety biomarker candidates that included various steroids and amino acids were discovered as a result of global metabolic profiling, and they were also confirmed by targeted metabolic profiling using gas chromatography/mass spectrometry (GC/MS) and capillary electrophoresis/mass spectrometry (CE/MS). Serum biochemical and histopathological tests were used to detect abnormal drug reactions in the liver after repeating oral administration of atorvastatin. The metabolic differences between control and the drug-treated groups were compared using PLS-DA score plots. These results were compared with the physiological and plasma biochemical parameters and the results of a histopathological test. Estrone, cortisone, proline, cystine, 3-ureidopropionic acid and histidine were proposed as potential safety biomarkers related with the liver toxicity of atorvastatin. These results indicate that the combined application of global and targeted metabolic profiling could be a useful tool for the discovery of drug safety biomarkers.