Relative quantification of erythropoietin receptor-dependent phosphoproteins using in-gel 18O-labeling and tandem mass spectrometry

On examining different proteomics approaches for the investigation of structure-function relationships of erythropoietin (EPO) receptor signaling, it was found that two-dimensional gel electrophoresis/mass spectrometry procedures are clearly limited in their ability to detect low-expressed signaling proteins. Instead it was found that a strategy involving anti-phosphotyrosine immunoprecipitation, one-dimensional gel electrophoresis (1DE), and capillary liquid chromatography/tandem mass spectrometry (LC/MS/MS) provides the sensitivity required for identification of signaling proteins. In the present work the immunoprecipitation/1DE/LC/MS approach was combined with an in-gel 18O-labeling technique to analyze EPO receptor-dependent proteins. Identification and relative quantification of more than 180 EPO receptor-dependent proteins were achieved directly based on the in-gel 18O-labeling approach.     

A combination of chemical derivatisation and improved bioinformatic tools optimises protein identification for proteomics

The identification of individual protein species within an organism's proteome has been optimised by increasing the information produced from mass spectral analysis through the chemical derivatisation of tryptic peptides and the development of new software tools. Peptide fragments are subjected to two forms of derivatisation. First, lysine residues are converted to homoarginine moieties by guanidination. This procedure has two advantages, first, it usually identifies the C-terminal amino acid of the tryptic peptide and also greatly increases the total information content of the mass spectrum by improving the signal response of C-terminal lysine fragments. Second, an Edman-type phenylthiocarbamoyl (PTC) modification is carried out on the N-terminal amino acid. The renders the first peptide bond highly susceptible to cleavage during mass spectrometry (MS) analysis and consequently allows the ready identification of the N-terminal residue. The utility of the procedure has been demonstrated by developing novel bioinformatic tools to exploit the additional mass spectral data in the identification of proteome proteins from the yeast Saccharomyces cerevisiae. With this combination of novel chemistry and bioinformatics, it should be possible to identify unambiguously any yeast protein spot or band from either two-dimensional or one-dimensional electropheretograms.     

MSQ: a tool for quantification of proteomics data generated by a liquid chromatography/matrix‐assisted laser desorption/ionization time‐of‐flight tandem mass spectrometry based targeted quantitative proteomics platform

Mass spectrometry (MS)‐based quantitative proteomics has become a critical component of biological and clinical research for identification of biomarkers that can be used for early detection of diseases. In particular, MS‐based targeted quantitative proteomics has been recently developed for the detection and validation of biomarker candidates in complex biological samples. In such approaches, synthetic reference peptides that are the stable isotope labeled version of proteotypic peptides of proteins to be quantitated are used as internal standards enabling specific identification and absolute quantification of targeted peptides. The quantification of targeted peptides is achieved using the intensity ratio of a native peptide to the corresponding reference peptide whose spike‐in amount is known. However, a manual calculation of the ratios can be time‐consuming and labor‐intensive, especially when the number of peptides to be tested is large. To establish a liquid chromatography/matrix‐assisted laser desorption/ionization time‐of‐flight tandem mass spectrometry (LC/MALDI TOF/TOF)‐based targeted quantitative proteomics pipeline, we have developed a software named Mass Spectrometry based Quantification (MSQ). This software can be used to automate the quantification and identification of targeted peptides/proteins by the MALDI TOF/TOF platform. MSQ was applied to the detection of a selected group of targeted peptides in pooled human cerebrospinal spinal fluid (CSF) from patients with Alzheimer's disease (AD) in comparison with age‐matched control (OC). The results for the automated quantification and identification of targeted peptides/proteins in CSF were in good agreement with results calculated manually. Copyright © 2010 John Wiley & Sons, Ltd.     

Recently developed GC/MS and LC/MS methods for determining NSAIDs in water samples

Pharmaceuticals have become major targets in environmental chemistry due to their presence in aquatic environments (following incomplete removal in wastewater treatment or point-source contaminations), threat to drinking water sources and concern about their possible effects to wildlife and humans. Recently several methods have been developed for the determination of drugs and their metabolites in the lower nanogram per litre range, most of them using solid-phase extraction (SPE) or solid-phase microextraction (SPME), derivatisation and finally gas chromatography mass spectrometry (GC-MS), gas chromatography tandem mass spectrometry (GC-MS/MS) and liquid chromatography electrospray tandem mass spectrometry (LC-ES/MS/MS). Due to the elevated polarity of non-steroidal anti-inflamatory drugs (NSAIDs), analytical techniques based on either liquid chromatography coupled to mass spectrometry (LC-MS) and gas chromatography coupled to mass spectrometry (GC-MS) after a previous derivatisation step are essential. The most advanced aspects of current GC-MS, GC-MS/MS and LC-MS/MS methodologies for NSAID analysis are presented.     

MASSyPup — an ‘Out of the Box’ solution for the analysis of mass spectrometry data

Mass spectrometry has evolved to a key technology in the areas of metabolomics and proteomics. Centralized facilities generate vast amount of data, which frequently need to be processed off‐site. Therefore, the distribution of data and software, as well as the training of personnel in the analysis of mass spectrometry data, becomes increasingly important. Thus, we created a comprehensive collection of mass spectrometry software which can be run directly from different media such as DVD or USB without local installation. MASSyPup is based on a Linux Live distribution and was complemented with programs for conversion, visualization and analysis of mass spectrometry (MS) data. A special emphasis was put on protein analysis and proteomics, encompassing the measurement of complete proteins, the identification of proteins based on Peptide Mass Fingerprints (PMF) or LC‐MS/MS data, and de novo sequencing. Another focus was directed to the study of metabolites and metabolomics, covering the detection, identification and quantification of compounds, as well as subsequent statistical analyses. Additionally, we added software for Mass Spectrometry Imaging (MSI), including hardware support for self‐made MSI devices. MASSyPup represents a ‘ready to work’ system for teaching or MS data analysis, but also represents an ideal platform for the distribution of MS data and the development of related software. The current Live DVD version can be downloaded free of charge from http://www.bioprocess.org/massypup . Copyright © 2014 John Wiley & Sons, Ltd.     

Applications of Tandem Mass Spectrometry (MS/MS) in Protein Analysis for Biomedical Research

Mass Spectrometry (MS) allows the analysis of proteins and peptides through a variety of methods, such as Electrospray Ionization-Mass Spectrometry (ESI-MS) or Matrix-Assisted Laser Desorption Ionization-Mass Spectrometry (MALDI-MS). These methods allow identification of the mass of a protein or a peptide as intact molecules or the identification of a protein through peptide-mass fingerprinting generated upon enzymatic digestion. Tandem mass spectrometry (MS/MS) allows the fragmentation of proteins and peptides to determine the amino acid sequence of proteins (top-down and middle-down proteomics) and peptides (bottom-up proteomics). Furthermore, tandem mass spectrometry also allows the identification of post-translational modifications (PTMs) of proteins and peptides. Here, we discuss the application of MS/MS in biomedical research, indicating specific examples for the identification of proteins or peptides and their PTMs as relevant biomarkers for diagnostic and therapy.     

Targeted comparative proteomics by liquid chromatography/matrix-assisted laser desorption/ionization triple-quadrupole mass spectrometry

Here we report the first application of a matrix-assisted laser desorption/ionization (MALDI) triple-quadrupole mass spectrometer for targeted proteomics. Employing an amine-specific isotopic labelling approach, the technique was validated using five randomly selected bovine serum albumin peptides differentially labelled at known ratios. An indirect benefit of the isotopic labelling technique is a significant enhancement of the a1 ion in tandem mass (MS/MS) spectra of all peptides studied. Therefore, the a1 ion was selected as the fragment ion for multiple reaction monitoring (MRM) in all cases, eliminating tedious method development and optimization. Accurate quantification was achieved with an average relative standard deviation (RSD) of 5% (n = 5) and a detection limit of 14 amol. The technique was then applied to validate an important virulence biomarker of the fungal pathogen Candida albicans, which was not accurately quantified using global proteomics experiment employing two-dimensional liquid chromatography/electrospray ionization tandem mass spectrometry (2D-LC/ESI)-MS/MS. Using LC/MALDI-MRM analysis of five tryptic peptides, the protein PHR1 was found to be upregulated in the hyphal (pathogenic) form of C. albicans by a factor of 7.7 +/- 0.8.     

ESI-MS/MS analysis of underivatised amino acids: a new tool for the diagnosis of inherited disorders of amino acid metabolism. Fragmentation study of 79 molecules of biological interest in positive and negative ionisation mode

The diagnosis of inherited disorders of amino acids (AA) metabolism is usually performed on automated analysers by ion-exchange chromatography and quantification after ninhydrin derivatisation of about 50 different AA. A single run liquid chromatography/tandem mass spectrometry (LC/MS/MS) method for these molecules can be an alternative to this time-consuming technique. The first step of this development is the infusion study of the fragmentation of 79 molecules of biological interest in electrospray ionisation tandem mass spectrometry (ESI-MS/MS), in positive and in negative ionisation mode. Among them, three molecules can be detected only in negative ionisation mode, 38 only in positive mode and 38 in the two modes. All the most abundant fragmentations are presented, with optimisation of the MS/MS parameters. The positive ionisation mode was retained for the simultaneous analysis of 76 molecules. One sensitive and/or specific transition is proposed for the monitoring of each molecule. Improvement in sensitivity of detection was obtained with the use of an acidic mobile phase. Flow injection analysis studies led us to highlight a number of interferences-due to isobaric molecules, to in-source collision-induced dissociation, or to natural isotopic distribution of the elements-which are listed. For a reliable quantification method, these molecules have to be separated by LC before analysis in the tandem mass spectrometer. Ion-pairing reversed-phase liquid chromatography (RPLC) using perfluorinated carboxylic acids as ion-pairing agents has already been found suitable for analysis of AA in MS/MS positive ionisation mode and is under development.     

A multiresidue method using ion-trap gas chromatography–tandem mass spectrometry with or without derivatisation with pentafluorobenzylbromide for the analysis of pesticides in the atmosphere

A multiresidue method using gas chromatography coupled to ion-trap tandem mass spectrometry (MS/MS) was developed for the analysis of 27 pesticides, commonly used in Alsace, in atmospheric samples (particle and gas phases). As pesticides are expected to be present at very low concentrations and in a complex matrix, the analytical method used was both highly selective and sensitive. These two properties were obtained by associating chromatography with ion-trap MS/MS. To develop this method, analysis of electron impact in single MS was first conducted to choose the parent ions of the pesticides studied. Among the 27 pesticides analysed, seven of them require a derivatisation step. This was the case of some ureas (chlorotoluron, diuron and isoproturon), phenoxy acids (2,4-dichlorophenoxyacetic acid, 4-chloro-2-methylphenoxyacetic acid and mecoprop) and of bromoxynil. The derivatisation was performed with success with pentafluorobenzylbromide. Then, a MS/MS method was optimised by parameters such as the radio frequency storage level and the collision-induced dissociation excitation voltage. Finally, a last step enabled the development of two calibrating programs based on the quantification of daughter ions for the 20 pesticides analysed directly (run 1) and for the seven pesticides which needed derivatisation (run 2). With this analytical procedure, the detection limits varied between 2.5 and 1,250 pg m^–3 depending on the compounds studied. This method was tested with success for atmospheric samples collected in Strasbourg (France) during intensive pesticide treatment in 2002.     

Advances in analytical methodology for bioinorganic speciation analysis: metallomics, metalloproteomics and heteroatom-tagged proteomics and metabolomics

The recent developments in analytical techniques capable of providing information on the identity and quantity of heteroatom-containing biomolecules are critically discussed. Particular attention is paid to the emerging areas of bioinorganic analysis including: (i) a comprehensive analysis of the entirety of metal and metalloid species within a cell or tissue type (metallomics), (ii) the study of the part of the metallome involving the protein ligands (metalloproteomics), and (iii) the use of a heteroelement, naturally present in a protein or introduced in a tag added by means of derivatisation, for the spotting and quantification of proteins (heteroatom-tagged proteomics). Inductively coupled plasma mass spectrometry (ICP MS), used as detector in chromatography and electrophoresis, and supported by electrospray and MALDI MS, appears as the linchpin analytical technique for these emerging areas. This review focuses on the recent advances in ICP MS in biological speciation analysis including sensitive detection of non-metals, especially of sulfur and phosphorus, couplings to capillary and nanoflow HPLC and capillary electrophoresis, laser ablation ICP MS detection of proteins in gel electrophoresis, and isotope dilution quantification of biomolecules. The paper can be considered as a followup of a previous review by the author on a similar topic (J. Szpunar, Analyst, 2000, 125, 963).     

Optimized orbitrap HCD for quantitative analysis of phosphopeptides

Despite the tremendous commercial success of radio frequency quadrupole ion traps for bottom-up proteomics studies, there is growing evidence that peptides decorated with labile post-translational modifications are less amenable to low-energy, resonate excitation MS/MS analysis. Moreover, multiplexed stable isotope reagents designed for MS/MS-based quantification of peptides rely on accurate and robust detection of low-mass fragments for all precursors. Collectively these observations suggest that beam-type or tandem in-space MS/MS measurements, such as that available on traditional triple quadrupole mass spectrometers, may provide beneficial figures of merit for quantitative proteomics analyses. The recent introduction of a multipole collision cell adjacent to an Orbitrap mass analyzer provides for higher energy collisionally activated dissociation (HCD) with efficient capture of fragment ions over a wide mass range. Here we describe optimization of various instrument and post-acquisition parameters that collectively provide for quantification of iTRAQ-labeled phosphorylated peptides isolated from complex cell lysates. Peptides spanning a concentration dynamic range of 100:1 are readily quantified. Our results indicate that appropriate parameterization of collision energy as a function of precursor m/z and z provides for optimal performance in terms of peptide identification and relative quantification by iTRAQ. Using this approach, we readily identify activated signaling pathways downstream of oncogenic mutants of Flt-3 kinase in a model system of human myeloid leukemia.     

Extraction of perfluorinated compounds from food matrices using fluorous solvent partitioning

Perfluorinated compounds (PFCs) such as perfluorooctane sulfonic acid (PFOS) have emerged as a new class of global environmental pollutant; they bioaccumulate and are persistent in the environment and in wildlife. Fluorine-fluorine interactions have been investigated as a means to isolate PFCs for mass spectrometric quantification. A novel sample extraction and cleanup procedure has been developed for fat-containing samples based on fluorous liquid-liquid extraction (F-LLE) in a triphasic solvent system consisting of hybrid:fluorous:organic solvent (trifluoroethanol:perfluorohexane/dichloromethane-saturated with water). This system partially separates fluorous from non-fluorous compounds, allowing removal of co-extractants, which had previously resulted in liquid chromatography mass spectrometry (LC-MS/MS) peak suppression preventing low-level detection of PFCs. The developed F-LLE was coupled with an existing extraction protocol allowing the limits of detection of PFCs to be lowered an order of magnitude for high fat samples. The developed workflow was used to show the absence of a range of eleven PFCs in nine UK and one Irish cheese samples. This representative application demonstrates a new application of fluorous-organic extraction in sample cleanup for measurement of fluorinated analytes in food, environment and broader analytical chemistry.     

Critical review of the application of liquid chromatography/mass spectrometry to the determination of pesticide residues in biological samples

A critical review is made on the use of hyphenated liquid chromatography/mass spectrometry (LC–MS) for the identification and quantification of pesticides and their metabolites in human biosamples (whole blood, plasma, serum and urine). The first applications of LC–MS in this field began in the early 1990s. Since then, increasing interest has been shown in applying this powerful technique, with most applications dealing with the determination of a variety of chemically diverse metabolites in urine. The use of different LC–MS interfaces and mass spectral detection modes are discussed. Special attention is given to tandem mass spectrometry (MS/MS) due to its inherent advantages of increased sensitivity and selectivity, as well as its advantages for identification and confirmation of analytes in samples. Quantification can be severely affected by matrix effects, the most common being inhibition of the ionisation of analytes in the mass spectrometer, which leads to unacceptable errors if no correction is made. Different approaches can be employed to minimise this undesirable matrix effect, the preferred being the use of labelled internal standards (when available) in isotope dilution methods or the application of an efficient clean-up, performed off-line or automated on-line. Adequate criteria for confirming the identities of residues detected are required in order to avoid false positives. The criterion most commonly used with a triple quadrupole instrument is the monitoring of two MS/MS transitions together with the ion abundance ratio. TOF mass analysers are seldom used in pesticide residue analysis despite their improved resolution and mass accuracy characteristics, which makes them very suitable for confirmation purposes. The main reasons for the relative unpopularity of TOF MS in residue analysis are its limited sensitivity and its high acquisition cost. In this paper, we present a critical assessment on current techniques, trends and future developments, and give illustrative examples to point out the main characteristics of LC–MS for pesticide residue analysis in biological fluids.     

Derivatisation for the characterisation of neutral oxosteroids by electrospray and matrix-assisted laser desorption/ionisation tandem mass spectrometry: the Girard P derivative

The identification, quantification and localisation of steroids in biological fluids and tissues are subjects of considerable importance. Not only do steroids have classical hormonal properties via binding to nuclear receptors, they can also elicit cellular responses via interactions with other proteins. For mass spectrometric analysis, neutral steroids are not readily ionised by either electrospray (ES) or matrix-assisted laser desorption/ionisation (MALDI). In this communication a derivatisation protocol is presented which allows for the rapid analysis of neutral oxosteroids by both ES and MALDI mass spectrometry. Neutral oxosteroids are derivatised to Girard P hydrazones. When analysed by tandem mass spectrometry the derivatised steroids fragment to give structurally informative spectra allowing subsequent steroid identification. The derivatisation method is simple, the reagents are commercially available, and reaction products are easily isolated from the reaction mixture. Analyte identification can be performed at the sub-pg level.     

How many proteins can be identified in a 2DE gel spot within an analysis of a complex human cancer tissue proteome?

Two‐dimensional gel electrophoresis (2DE) in proteomics is traditionally assumed to contain only one or two proteins in each 2DE spot. However, 2DE resolution is being complemented by the rapid development of high sensitivity mass spectrometers. Here we compared MALDI‐MS, LC‐Q‐TOF MS and LC‐Orbitrap Velos MS for the identification of proteins within one spot. With LC‐Orbitrap Velos MS each Coomassie Blue‐stained 2DE spot contained an average of at least 42 and 63 proteins/spot in an analysis of a human glioblastoma proteome and a human pituitary adenoma proteome, respectively, if a single gel spot was analyzed. If a pool of three matched gel spots was analyzed this number further increased up to an average of 230 and 118 proteins/spot for glioblastoma and pituitary adenoma proteome, respectively. Multiple proteins per spot confirm the necessity of isotopic labeling in large‐scale quantification of different protein species in a proteome. Furthermore, a protein abundance analysis revealed that most of the identified proteins in each analyzed 2DE spot were low‐abundance proteins. Many proteins were present in several of the analyzed spots showing the ability of 2DE‐MS to separate at the protein species level. Therefore, 2DE coupled with high‐sensitivity LC‐MS has a clearly higher sensitivity as expected until now to detect, identify and quantify low abundance proteins in a complex human proteome with an estimated resolution of about 500 000 protein species. This clearly exceeds the resolution power of bottom‐up LC‐MS investigations.     

Edman降解中异硫氰酸苯酯新修饰位点的发现和验证

Edman降解是最早建立的一种用于多肽和蛋白质氨基端测序的方法,该方法现在仍被广泛用于生物化学领域。随着高通量蛋白质组学技术的发展和应用,该方法中的异硫氰酸苯酯反应被用于修饰蛋白质氨基端,并用于检测蛋白质水解位点。但还没有异硫氰酸苯酯是否可以修饰其他氨基酸侧链并影响多肽序列分析的研究。为了探究其修饰其他氨基酸的可能性,本文利用基质辅助激光解吸电离飞行时间质谱（MALDI-TOF-MS）和液相色谱-串联质谱（LC-MS/MS）研究了异硫氰酸苯酯对一个模型肽的化学修饰。质谱数据解析后发现在高浓度异硫氰酸苯酯的反应条件下,组氨酸上可以引入一个新的异硫氰酸苯酯修饰位点。这一修饰位点的发现预示着通过改变实验条件或分析方法,可以更准确地利用Edman降解和蛋白质组学技术分析多肽和蛋白质。     

Potential of MALDI-TOF mass spectrometry as a rapid detection technique in plant pathology: identification of plant-associated microorganisms

Plant diseases caused by plant pathogens substantially reduce crop production every year, resulting in massive economic losses throughout the world. Accurate detection and identification of plant pathogens is fundamental to plant pathogen diagnostics and, thus, plant disease management. Diagnostics and disease-management strategies require techniques to enable simultaneous detection and quantification of a wide range of pathogenic and non-pathogenic microorganisms. Over the past decade, rapid development of matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) techniques for characterization of microorganisms has enabled substantially improved detection and identification of microorganisms. In the biological sciences, MALDI-TOF MS is used to analyze specific peptides or proteins directly desorbed from intact bacteria, fungal spores, nematodes, and other microorganisms. The ability to record biomarker ions, in a broad m/z range, which are unique to and representative of individual microorganisms, forms the basis of taxonomic identification of microorganisms by MALDI-TOF MS. Recent advances in mass spectrometry have initiated new research, i.e. analysis of more complex microbial communities. Such studies are just beginning but have great potential for elucidation not only of the interactions between microorganisms and their host plants but also those among different microbial taxa living in association with plants. There has been a recent effort by the mass spectrometry community to make data from large scale mass spectrometry experiments publicly available in the form of a centralized repository. Such a resource could enable the use of MALDI-TOF MS as a universal technique for detection of plant pathogens and non-pathogens. The effects of experimental conditions are sufficiently understood, reproducible spectra can be obtained from computational database search, and microorganisms can be rapidly characterized by genus, species, or strain.     

蛋白质组的分离与分析及其应用进展

蛋白质组学正在成为分析化学研究的热点。本文综述了蛋白质组的高通量分离和分析技术，包括双向凝胶电泳、生物质谱、二维谱新技术和蛋白芯片的发展现状以及蛋白质组学的最新应用进展，并展望了分析化学在蛋白质组学领域今后的发展。     

Surface plasmon resonance imaging in arrays coupled with mass spectrometry (SUPRA–MS): proof of concept of on-chip characterization of a potential breast cancer marker in human plasma

Protein biomarker discovery and validation are crucial for diagnosis, prognosis, and theranostics of human pathologies; "omics" approaches bring new insights in this field. In particular, the combination of immuno-sensors in array format with mass spectrometry efficiently extends the classical immunoassay format and includes molecular characterization. Here, we coupled surface plasmon resonance imaging (SPRi) with MALDI-TOF mass spectrometry in a hyphenated technique which enables multiplexed quantification of binding by SPRi and molecular characterization of interacting partners by subsequent MS analysis. This adds specificity, because MS enables differentiation of molecules that are difficult to distinguish by use of antibodies, for example truncation variants or protein isoforms. Proof of concept was established for detection, identification, and characterization of a potential breast cancer marker, the LAG3 protein, at ~1?μg?mL(-1), added to human plasma. The analytical performance of this new method, dubbed "SUPRA-MS", was established, particularly its specificity (S/N > 10) and reliability (100?% LAG3 identification with high significant mascot score >87.9). The adjusted format for rapid, collective, and automated on-chip MALDI-MS analysis is robust at the femtomole level and has numerous potential applications in proteomics.     

Validation of a gas chromatography/triple quadrupole mass spectrometry based method for the quantification of pesticides in food commodities

A new multiresidue method has been validated in cucumber matrix for the routine analysis of 130 multiclass pesticide residues by gas chromatography/triple quadrupole mass spectrometry. The pesticides were extracted with ethyl acetate. A first identification of the pesticides was based on a tandem mass spectrometric (MS/MS) screening method, which monitors a single transition for each target compound, in less than 12 min. After that, potentially non-negative samples were analyzed again by the MS/MS confirmation/quantification method, which monitors two or three MS/MS transitions for each compound, also in less than 12 min. Performance characteristics, such as trueness, precision, linear range, detection limit (LOD) and quantification limit (LOQ), for each pesticide were calculated. The average recoveries obtained ranged between 70 and 120% at three different fortification levels (25, 200 and 500 microg/kg) with precision, expressed as relative standard deviation (RSD), values lower than 15%. The calculated LOD and LOQ were typically <3.2 and 9.6 microg/kg, respectively. Such limits were much lower than the maximum residue levels (MRLs) established by European legislation. The proposed methodology was applied to the determination of pesticides in real vegetable samples from Almería (Spain).