MS-based Techniques Research Articles

Peptide mapping during dynamic gastric digestion of heated and unheated skimmed milk powder

This study aims to evaluate the impact of heat treatment on the hydrolysis kinetics of cow milk proteins and on the peptide release during in vitro dynamic gastric digestion. SDS-PAGE and ELISA techniques were employed to assess the hydrolysis of proteins over time of digestion. The evolution of the peptidome generated through dynamic digestion of heated and non-heated milk was studied at different times, using MS-based techniques (ion trap and MALDI-TOF/TOF) coupled to liquid chromatography. The peptide homology value between both samples at the end of digestion (48%) confirmed the impact of heat treatment on the identity of peptides generated during digestion, despite their identical initial protein content and being the same matrix in both cases. Heat treatment produced an increased resistance to hydrolysis by pepsin in the casein fraction. However, β-lactoglobulin was found to be more susceptible to hydrolysis. Although differences on the pattern of peptide release were found between both samples, also some common traits after digestion were observed. The regions comprised between the residues 76–93 of β-casein, where several binding epitopes are included, as well as the β-casein domains 126–140 and 190–209 were found to be resistant to pepsin.

Mass spectrometric based approaches in urine metabolomics and biomarker discovery.

Urine metabolomics has recently emerged as a prominent field for the discovery of non-invasive biomarkers that can detect subtle metabolic discrepancies in response to a specific disease or therapeutic intervention. Urine, compared to other biofluids, is characterized by its ease of collection, richness in metabolites and its ability to reflect imbalances of all biochemical pathways within the body. Following urine collection for metabolomic analysis, samples must be immediately frozen to quench any biogenic and/or non-biogenic chemical reactions. According to the aim of the experiment; sample preparation can vary from simple procedures such as filtration to more specific extraction protocols such as liquid-liquid extraction. Due to the lack of comprehensive studies on urine metabolome stability, higher storage temperatures (i.e. 4°C) and repetitive freeze-thaw cycles should be avoided. To date, among all analytical techniques, mass spectrometry (MS) provides the best sensitivity, selectivity and identification capabilities to analyze the majority of the metabolite composition in the urine. Combined with the qualitative and quantitative capabilities of MS, and due to the continuous improvements in its related technologies (i.e. ultra high-performance liquid chromatography [UPLC] and hydrophilic interaction liquid chromatography [HILIC]), liquid chromatography (LC)-MS is unequivocally the most utilized and the most informative analytical tool employed in urine metabolomics. Furthermore, differential isotope tagging techniques has provided a solution to ion suppression from urine matrix thus allowing for quantitative analysis. In addition to LC-MS, other MS-based technologies have been utilized in urine metabolomics. These include direct injection (infusion)-MS, capillary electrophoresis-MS and gas chromatography-MS. In this article, the current progresses of different MS-based techniques in exploring the urine metabolome as well as the recent findings in providing potentially diagnostic urinary biomarkers are discussed. © 2015 Wiley Periodicals, Inc. Mass Spec Rev 36:115-134, 2017.

Mass spectrometry coupled to imaging techniques: the better the view the greater the challenge.

These are definitively exciting times for membrane lipid researchers. Once considered just as the cell membrane building blocks, the important role these lipids play is steadily being acknowledged. The improvement occurred in mass spectrometry techniques (MS) allows the establishment of the precise lipid composition of biological extracts. However, to fully understand the biological function of each individual lipid species, we need to know its spatial distribution and dynamics. In the past 10 years, the field has experienced a profound revolution thanks to the development of MS-based techniques allowing lipid imaging (MSI). Images reveal and verify what many lipid researchers had already shown by different means, but none as convincing as an image: each cell type presents a specific lipid composition, which is highly sensitive to its physiological and pathological state. While these techniques will help to place membrane lipids in the position they deserve, they also open the black box containing all the unknown regulatory mechanisms accounting for such tailored lipid composition. Thus, these results urges to different disciplines to redefine their paradigm of study by including the complexity revealed by the MSI techniques.

Plant hormone signalling through the eye of the mass spectrometer.

Plant growth and development are regulated by hormones and the associated signalling pathways share several common steps, the first being the detection of the signal by receptor proteins. This typically leads to conformational changes in the receptor, thereby modifying its spectrum of interaction partners. Next, secondary signals are transmitted via rapid post-translational cascades, such as targeted phosphorylation or ubiquitination, resulting in the activation/deactivation, relocalization or degradation of target proteins. These events finally give rise to the signal-dependent read-out, such as changes in gene expression and regulation of protein activity. So far, the majority of studies aimed at unravelling hormone signalling pathways in plants relied on genetic or transcriptomic approaches. During the last decade however, MS-driven proteomic methods became increasingly popular tools in plant research as they reveal the specific mechanisms controlled by phytohormones, which for a large part occur on the level of the proteome. Here, we provide an up-to-date review on the growing body of work in these areas using MS-based techniques, with a focus on nonpeptide plant hormones.

SWATH-MS in proteomics: current status

Sequential window acquisition of all theoretical fragment ion spectra coupled to tandem mass spectrometry (SWATH-MS) is a new strategy for identification and quantification of proteins and proteomes proposed in 2012. SWATH-MS operates in unbiased data-independent acquisition (DIA) mode and combines the advantages of two widely used MS-based techniques: shotgun (high throughput) and SRM proteomics (high sensitivity and reproducibility). In this review, we provide an introduction of the SWATH-MS method, its application, and a perspective on the future of this powerful technology.

Mass Spectrometry-Based Proteomic Study Makes High-Density Lipoprotein a Biomarker for Atherosclerotic Vascular Disease.

High-density lipoprotein (HDL) is a lipid and protein complex that consists of apolipoproteins and lower level HDL-associated enzymes. HDL dysfunction is a factor in atherosclerosis and decreases patient survival. Mass spectrometry- (MS-) based proteomics provides a high throughput approach for analyzing the composition and modifications of complex HDL proteins in diseases. HDL can be separated according to size, surface charge, electronegativity, or apoprotein composition. MS-based proteomics on subfractionated HDL then allows investigation of lipoprotein roles in diseases. Herein, we review recent developments in MS-based quantitative proteomic techniques, HDL proteomics and lipoprotein modifications in diseases, and HDL subfractionation studies. We also discuss future directions and perspectives in MS-based proteomics on HDL.

Biomarker discovery in asthma and COPD by proteomic approaches.

Asthma and chronic obstructive pulmonary disease (COPD) are multifactorial respiratory diseases, characterized by reversible and irreversible airway obstruction, respectively. Even if the primary causes of these diseases remain unknown, inflammation is a central feature that leads to progressive and permanent pulmonary tissue damage (airway remodeling) up to the total loss of lung function. Therefore, the elucidation of the inflammation mechanisms and the characterization of the biological pathways, involved in asthma and COPD pathogenesis, are relevant in finding new possible diagnostic/prognostic biomarkers and for the validation of new drug targets. In this context, current advances in proteomic approaches, especially those based on MS, provide new tools to facilitate the discovery-driven studies of new biomarkers in respiratory diseases and improve the clinical reliability of the next generation of biomarkers for these diseases consisting of multiple phenotypes. This review will report an overview of the current proteomic methods applied to the discovery of candidate biomarkers for asthma and COPD, giving a special emphasis to emerging MS-based techniques.

A metabolomics approach shows that catechin-enriched green tea attenuates ultraviolet B-induced skin metabolite alterations in mice

In this study, catechin-enriched green tea (CGT) administration significantly attenuated ultraviolet (UV) B-induced mouse skin alterations, i.e., increases in wrinkle formation, thickness, erythema, and transepidermal water loss, and decreases in hydration, elasticity, and collagen fiber content. The metabolites in the mouse skin after UVB irradiation and CGT administration were profiled using comprehensive MS-based metabolomics techniques such as ultra-performance liquid chromatography-quadrupole time-of-flight-mass spectrometry (TOF-MS), gas chromatography-TOF-MS, and NanoMate tandem-MS. From these analysis, we revel that Normal, UVB-irradiated, and UVB-irradiated with CGT administrated groups clearly discriminated from each other in partial least squares-discriminant analysis models, and CGT administration attenuated UVB-induced alteration of skin metabolites such as lysophospholipids, fatty acids, ceramides, amino acids, organic compounds, lipids, and nucleobases. Among them, purine nucleobases (inosine and hypoxanthine), ascorbic acid, and lactose were remarkably influenced by CGT administration, which indicated that these metabolites could be biomarkers to explain CGT effects on UVB-irradiated skin. Our results suggested that CGT administration was effective in reducing the levels of UVB-induced alterations of numerous mouse skin metabolites, and these metabolites were might highly relevant to observed changes in skin conditions.

Recent advances in MS methods for nicotine and metabolite analysis in human matrices: clinical perspectives.

Tobacco smoking is a major global health issue and represents the leading cause of preventable death in the developed countries. Nicotine is a major alkaloid found in tobacco products and its detection with its metabolites in human matrices is generally used for assessing tobacco consumption and second hand exposure. Several analytical techniques have been developed for the detection of nicotine and its metabolites, and MS coupled with chromatography is considered the standard reference method because of its superior sensitivity and specificity. In this work, we reviewed nicotine metabolism, clinical MS and the latest (2009-2014) development of MS-based techniques for measurement of nicotine and metabolites in human matrices. Appropriate biomarker and matrix selection are also critically discussed.

A feasibility study to identify proteins in the residual Pap test fluid of women with normal cytology by mass spectrometry-based proteomics.

BackgroundThe proteomic analysis of body fluids is a growing technology for the identification of protein biomarkers of disease. Given that Papanicolaou tests (Pap tests) are routinely performed on over 30 million women annually in the U.S. to screen for cervical cancer, we examined the residual Pap test fluid as a source of protein for analysis by mass spectrometry (MS). In the liquid-based Pap test, cervical cells are collected from the ectocervix and placed into an alcohol-based fixative prior to staining and pathologic examination. We hypothesized that proteins shed by cells of the female genital tract can be detected in the Pap test fixative by MS-based proteomic techniques. We examined the feasibility of using residual fluid from discarded Pap tests with cytologically “normal” results to optimize sample preparation for MS analysis. The protein composition of the cell-free Pap test fluid was determined by silver staining of sodium dodecyl sulfate -polyacrylamide gels, and the abundance of serum proteins was examined by Western immunoblot using an antibody against human serum albumin. Both pooled and individual samples were trypsin digested and analyzed by two-dimensional MS/MS. Proteins were identified by searching against the Human Uniprot database, and characterized for localization, function and relative abundance.ResultsThe average volume of the residual Pap test fluid was 1.5 ml and the average protein concentration was 0.14 mg/ml. By Western immunoblot we showed that the amount of albumin in each sample was significantly reduced compared to normal serum. By MS/MS, we identified 714 unique proteins in pooled Pap test samples and an average of 431 proteins in individual samples. About 40% of the proteins identified were extracellular or localized to the plasma membrane. Almost 20% of the proteins identified were involved in immunity and defense, characteristic of the healthy cervical-vaginal proteome. By merging the protein sets from the individual and pooled Pap test samples, we created a “Normal Pap test Core Proteome” consisting of 153 proteins.ConclusionsResidual Pap test fluid contains a sufficient amount of protein for analysis by MS and represents a valuable biospecimen source for the identification of protein biomarkers for gynecological diseases.

Proteomic and other analyses to determine the functional consequences of deregulated kallikrein‐related peptidase (KLK) expression in prostate and ovarian cancer

Rapidly developing proteomic tools are improving detection of deregulated kallikrein-related peptidase (KLK) expression, at the protein level, in prostate and ovarian cancer, as well as facilitating the determination of functional consequences downstream. MS-driven proteomics uniquely allows for the detection, identification, and quantification of thousands of proteins in a complex protein pool, and this has served to identify certain KLKs as biomarkers for these diseases. In this review, we describe applications of this technology in KLK biomarker discovery and elucidate MS-based techniques that have been used for unbiased, global screening of KLK substrates within complex protein pools. Although MS-based KLK degradomic studies are limited to date, they helped to discover an array of novel KLK substrates. Substrates identified by MS-based degradomics are reported with improved confidence over those determined by incubating a purified or recombinant substrate and protease of interest, in vitro. We propose that these novel proteomic approaches represent the way forward for KLK research, in order to correlate proteolysis of biological substrates with tissue-related consequences, toward clinical targeting of KLK expression and function for cancer diagnosis, prognosis, and therapies.

The amyloid-β degradation pattern in plasma—A possible tool for clinical trials in Alzheimer's disease

Amyloid beta (Aβ) is the main component of plaques, the central neuropathological hallmark in Alzheimer's disease (AD). Aβ is derived from the amyloid precursor protein (APP) by β- and γ-secretase-mediated cleavages. A large number of Aβ peptides are found in cerebrospinal fluid and these peptides are produced in specific metabolic pathways, which are important for diagnosis, in drug development and to explore disease pathogenesis. To investigate whether a similar pattern could be found also in blood samples, an immunoprecipitation (IP) based method for enrichment of Aβ peptides from human plasma was developed. The peptides were analyzed using matrix-assisted-laser-desorption/ionization time-of-flight/time-of-flight mass spectrometry for Aβ profiling and selected reaction monitoring (SRM) for MS quantification of Aβ1-38, Aβ1-40 and Aβ1-42 using tripe quadrupole MS. Sixteen N- or C-terminally truncated Aβ peptides were reproducibly detected in human plasma, of which 11 were verified by tandem MS. In a pilot study including 9 AD patients and 10 controls, where Aβ1-38, Aβ1-40 and Aβ1-42 were quantified using SRM, no AD-associated change in plasma levels of the peptides were observed. Using MS-based measurement techniques, we show that several Aβ peptides can be monitored in a single analysis and the developed methods have the potential to be used as a read out in clinical trials of drugs affecting APP processing or Aβ homeostasis.

Stable Isotope Labeling of Phosphoproteins for Large-scale Phosphorylation Rate Determination

Signals that control responses to stimuli and cellular function are transmitted through the dynamic phosphorylation of thousands of proteins by protein kinases. Many techniques have been developed to study phosphorylation dynamics, including several mass spectrometry (MS)-based methods. Over the past few decades, substantial developments have been made in MS techniques for the large-scale identification of proteins and their post-translational modifications. Nevertheless, all of the current MS-based techniques for quantifying protein phosphorylation dynamics rely on the measurement of changes in peptide abundance levels, and many methods suffer from low confidence in phosphopeptide identification due to poor fragmentation. Here we have optimized an approach for the stable isotope labeling of amino acids by phosphate using [γ-¹⁸O₄]ATP in nucleo to determine global site-specific phosphorylation rates. The advantages of this metabolic labeling technique are increased confidence in phosphorylated peptide identification, direct labeling of phosphorylation sites, measurement phosphorylation rates, and the identification of actively phosphorylated sites in a cell-like environment. In this study we calculated approximate rate constants for over 1,000 phosphorylation sites based on labeling progress curves. We measured a wide range of phosphorylation rate constants from 0.34 min⁻¹ to 0.001 min⁻¹. Finally, we applied stable isotope labeling of amino acids by phosphate to identify sites that have different phosphorylation kinetics during G1/S and M phase. We found that most sites had very similar phosphorylation rates under both conditions; however, a small subset of sites on proteins involved in the mitotic spindle were more actively phosphorylated during M phase, whereas proteins involved in DNA replication and transcription were more actively phosphorylated during G1/S phase. The data have been deposited to the ProteomeXchange with the identifier PXD000680.

50 years of mass spectrometry at Firmenich: a continuing love story.

Mass spectrometry (MS) has been intensively used in the field of flavor and fragrance since its beginning in the 1950s, and it remains an essential technique for current and future research in this field. After a short historical section on the introduction and development of MS at Firmenich, this work reviews the main applications of MS-based techniques published by Firmenich researchers over the past 5 years. It exemplifies the use of gas chromatography (GC)-MS for the discovery of new odorant - hence volatile - molecules in a broad range of natural products, such as fruits, meats, and vegetables. Non-volatile compounds play a major role in taste attributes and are also possible precursors of odorant molecules. Their identification by liquid chromatography (LC)-MS in the context of malodor generation from sweat is a typical example of such a relationship. With their high selectivity and sensitivity, GC-MS and LC-MS instruments are used in the fields of flavor and fragrance not only for identification, but also as unique tools for the accurate quantitation of compounds in complex matrices. This is particularly important for regulatory analyses such as dosage of potential allergens in perfumes and for the development of delivery systems. Finally, because of the rapid response time of MS, the kinetics of processes such as the release of flavors in the mouth during food consumption can be monitored by direct sampling into the mass spectrometer.

Mapping orphan proteases by proteomics: Meprin metalloproteases deciphered as potential therapeutic targets

The protease web is a synonym for highly regulated molecular networks comprising enzymes, substrates, inhibitors, and other regulatory proteins. Latest high-throughput methods provided huge data sets, revealing an amazing complexity of proteolytic systems important for health and disease. Based on our previous studies, we discuss major problems and questions that have to be solved to gain precise insight into the regulation of the protease web and its impact on pathophysiological conditions. The goal is a combination of different proteomic approaches that help to investigate specific protease function at a glance. Exemplarily, the characterization of the metalloproteases meprin α and meprin β by proteomic identification of cleavage sites and terminal amine isotopic labeling of substrates demonstrates the power of MS-based techniques. Meprins are rather orphan proteases and could not be assigned to precise biological functions until recently. Proteomics helped to identify meprin α and meprin β being important for collagen assembly and deposition in skin, which makes them potential therapeutic targets in fibrotic conditions. Additionally, identification of the cleavage site specificity provides the basis for the development of activity-based probes and small compound inhibitors, important for the regulation of meprin activity and subsequent treatment of associated diseases.

Mass spectrometric characterization of the crustacean neuropeptidome

Neuropeptides (NPs) are the largest class of signaling molecules used by nervous systems. Despite their functional importance, numerous challenges exist to characterize the full complement of NPs – the neuropeptidome. In this review, we discuss recent advances in MS-based techniques for NP identification and quantitation, as well as sample preparation strategies for various applications in several crustacean model organisms. By surveying published examples of crustacean neuropeptidomic analyses, we highlight challenges and progress in this dynamic field, and summarize the current state of knowledge about crustacean NPs and MS-based methodologies for NP analysis.

Quantitative proteomics in the field of microbiology

Quantitative proteomics has become an indispensable analytical tool for microbial research. Modern microbial proteomics covers a wide range of topics in basic and applied research from in vitro characterization of single organisms to unravel the physiological implications of stress/starvation to description of the proteome content of a cell at a given time. With the techniques available, ranging from classical gel-based procedures to modern MS-based quantitative techniques, including metabolic and chemical labeling, as well as label-free techniques, quantitative proteomics is today highly successful in sophisticated settings of high complexity such as host-pathogen interactions, mixed microbial communities, and microbial metaproteomics. In this review, we will focus on the vast range of techniques practically applied in current research with an introduction of the workflows used for quantitative comparisons, a description of the advantages/disadvantages of the various methods, reference to hallmark publications and presentation of applications in current microbial research.

Peptidomics and processing of regulatory peptides in the fruit fly Drosophila

More than a decade has passed since the release of the Drosophila melanogaster genome and the first predictions of fruit fly regulatory peptides (neuropeptides and peptide hormones). Since then, mass spectrometry-based methods have fuelled the chemical characterisation of regulatory peptides, from 7 Drosophila peptides in the pre-genomic area to more than 60 today. We review the development of fruit fly peptidomics, and present a comprehensive list of the regulatory peptides that have been chemically characterised until today. We also summarise the knowledge on peptide processing in Drosophila, which has strongly profited from a combination of MS-based techniques and the genetic tools available for the fruit fly. This combination has a very high potential to study the functional biology of peptide signalling on all levels, especially with the ongoing developments in quantitative MS in Drosophila.

A device for single leaf labelling with CO2 isotopes to study carbon allocation and partitioning in Arabidopsis thaliana.

BackgroundPlant biomass consists primarily of carbohydrates derived from photosynthesis. Monitoring the assimilation of carbon via the Calvin-Benson cycle and its subsequent utilisation is fundamental to understanding plant growth. The use of stable and radioactive carbon isotopes, supplied to plants as CO2, allows the measurement of fluxes through the intermediates of primary photosynthetic metabolism, long-distance transport of sugars in the vasculature, and the synthesis of structural and storage components.ResultsHere we describe the design of a system for supplying isotopically labelled CO2 to single leaves of Arabidopsis thaliana. We demonstrate that the system works well using short pulses of 14CO2 and that it can be used to produce robust qualitative and quantitative data about carbon export from source leaves to the sink tissues, such as the developing leaves and the roots. Time course experiments show the dynamics of carbon partitioning between storage as starch, local production of biomass, and export of carbon to sink tissues.ConclusionThis isotope labelling method is relatively simple to establish and inexpensive to perform. Our use of 14CO2 helps establish the temporal and spatial allocation of assimilated carbon during plant growth, delivering data complementary to those obtained in recent studies using 13CO2 and MS-based metabolomics techniques. However, we emphasise that this labelling device could also be used effectively in combination with 13CO2 and MS-based techniques.

ChemInform Abstract: Application of Mass Spectrometric Techniques to Delineate the Modes‐of‐Action of Anticancer Metallodrugs

AbstractReview: 87 refs.