Mass Spectrometry-based Methodologies Research Articles

Multilevel human secondary lymphoid immune system compartmentalization revealed by complementary imaging approaches

Secondary human lymphoid tissue immune reactions take place in a highly coordinated environment with compartmentalization representing a fundamental feature of this organization. In situ profiling methodologies are indispensable for the understanding of this compartmentalization. Here, we propose a complementary experimental approach aiming to reveal different aspects of this process. The analysis of human tonsils, using a combination of single cell phenotypic analysis based on flow cytometry and multiplex imaging and mass spectrometry-based methodologies, revealed a compartmentalized organization at the cellular and molecular levels. More specifically, the skewed distribution of highly specialized immune cell subsets and relevant soluble mediators was accompanied by a compartmentalized localization of several lipids across different anatomical areas of the tonsillar tissue. The performance of such combinatorial experimental approaches could lead to the identification of novel in situ interactions and molecular targets for the invivo manipulation of lymphoid organ, particularly the germinal center, immune reactions.

Protein-Metabolite Interactions: Discovery and Significance.

Metabolites orchestrate cellular processes as either substrates, co-enzymes, inhibitors, or activators of cellular proteins such as enzymes and receptors. Although traditional biochemical and structural biology-based approaches have been successfully employed for the discovery of protein-metabolite interactions, they often fail to detect transient and low-affinity biomolecular relationships. Another limitation of these approaches is that they are performed under in vitro conditions lacking the physiological context. Recently developed mass spectrometry-based methodologies overcome both these shortcomings, and have resulted in the discovery of global protein-metabolite cellular interaction networks. Herein, we describe traditional and modern approaches for the discovery of protein-metabolite interactions, and discuss the impact of these discoveries on our understanding of cellular physiology and on drug development.

Analysis of highly polar pesticides in foods by LC-MS/MS.

Highly polar pesticides (HPP) are a group of pesticides that are characterize as low Log Kow. Many high-throughput multi-residue analysis methods based on liquid chromatography-tandem mass spectrometry (LC-MS/MS) for the simultaneous determination of such polar pesticides have been proposed. In this article, we summarize the various sample preparation methods including quick polar pesticides (QuPPe), dispersive solid phase extraction (dSPE), solid phase extraction (SPE) and QuEChERS (Quick, Easy, Cheap, Effective, Rugged and Safe), especially for QuPPe, which are mainly used for the determination of HPP in foods. In addition, we summarize LC-based separation methodologies that are currently used for the analysis of HPP in foods, including reversed-phase chromatography (RPC), hydrophilic interaction liquid chromatography (HILIC), ion chromatography (IC) and mixed-mode chromatography (MMC). Finally, the current mass spectrometry-based methodologies for the analysis of HPP are summarized with a specific focus on MS configurations and acquisition modes.

Identification of MAMP-Responsive Plasma Membrane-Associated Proteins in Arabidopsis thaliana Following Challenge with Different LPS Chemotypes from Xanthomonas campestris.

Lipopolysaccharides (LPS) are recognized as microbe-associated molecular patterns (MAMPs) responsible for eliciting defense-related responses and while the effects have been well-documented in mammals, there is a lack of knowledge regarding the mechanism of perception in plant systems and recognized structural moieties within the macromolecular lipoglycan structure. Thus, identification of the LPS plasma membrane (PM) receptor(s)/receptor complex in Arabidopsis thaliana through proteomics will contribute to a deeper understanding of induced defense responses. As such, structurally characterized LPS chemotypes from Xanthomonas campestris pv. campestris (Xcc) wild-type 8004 (prototypical smooth-type LPS) and mutant 8530 (truncated core with no O–chain) strains were utilized to pre-treat A. thaliana plants. The associated proteomic response/changes within the PM were compared over a 24 h period using mass spectrometry-based methodologies following three variants of LPS-immobilized affinity chromatography. This resulted in the identification of proteins from several functional categories, but importantly, those involved in perception and defense. The distinct structural features between wild-type and mutant LPS are likely responsible for the differential changes to the proteome profiles, and many of the significant proteins were identified in response to the wild-type Xcc LPS where it is suggested that the core oligosaccharide and O-chain participate in recognition by receptor-like kinases (RLKs) in a multiprotein complex and, notably, varied from that of the mutant chemotype.

16α-Hydroxyestrone: Mass Spectrometry-Based Methodologies for the Identification of Covalent Adducts Formed with Blood Proteins.

Elevated levels of the estrone metabolite, 16α-hydroxyestrone (16αOHE1), have been linked with multiple diseases. As an electrophilic reactive metabolite, covalent binding to proteins is thought to constitute one of the possible mechanisms in the onset of deleterious health outcomes associated with 16αOHE1. Whereas mass spectrometry (MS)-based methodologies are currently considered the best suited to monitor the formation of protein covalent adducts, the application of these approaches for the identification of covalent adducts of 16αOHE1 is yet to be provided. In the present study, with the ultimate goal of determining the most adequate methodology for searching for 16αOHE1-derived covalent adducts, we explored multiple liquid chromatography-electrospray ionization tandem high-resolution mass spectrometry (LC-ESI-HRMS/MS)-based approaches to investigate the nature and specific locations of the covalent adducts produced in human hemoglobin (Hb) and human serum albumin (HSA) modified in vitro with 16αOHE1. The application of a "bottom up" proteomics approach, involving the nanoLC-ESI-HRMS/MS analysis of tryptic peptides, allowed the identification of multiple sites of 16αOHE1 adduction in Hb and HSA. As expected, the majority of the adducted peptides occurred in lysine residues following stabilization of the Schiff base formed with 16αOHE1 by reduction or via Heyns rearrangement, yielding the stable α-hydroxyamine and ketoamine adducts, respectively. Noteworthy is the fact that a serine residue was also identified to be covalently modified with 16αOHE1, which to our knowledge constitutes a first-hand report of a keto electrophile as target of hydroxyl-based nucleophilic amino acids. The N-alkyl Edman degradation resulted to be unsuitable for the identification of 16αOHE1adducts formed with the N-terminal valine of Hb, most probably due to stereochemical restraints of the tested derivatizing agents (fluorescein isothiocyanate and phenyl isothiocyanate) on assessing these bulky covalent adducts. Nonetheless, the digestion of adducted proteins to amino acids resulted in the detection of 16αOHE1-derived keto and α-hydroxyamine Lys adducts. The simplicity of this methodology might be beneficial for clinical studies, with the possibility of offering quantitative information with the preparation of synthetic standards of these adducts. The results obtained are crucial not only for the identification and quantification of biomarkers of exposure to 16αOHE1 but also for clarifying the role of protein binding in the onset of diseases associated with elevated levels of this reactive metabolite.

Localization of Double Bonds in Bacterial Glycerophospholipids Using 193 nm Ultraviolet Photodissociation in the Negative Mode.

The need for detailed structural characterization of glycerophospholipids (GPLs) for many types of biologically motivated applications has led to the development of novel mass spectrometry-based methodologies that utilize alternative ion activation methods. Ultraviolet photodissociation (UVPD) has shown great utility for localizing sites of unsaturation within acyl chains and to date has predominantly been used for positive mode analysis of GPLs. In the present work, UVPD is used to localize sites of unsaturation in GPL anions. Similar to UVPD mass spectra of GPL cations, UVPD of deprotonated or formate-adducted GPLs yields diagnostic fragment ions spaced 24 Da apart. This method was integrated into a liquid chromatography workflow and used to evaluate profiles of sites of unsaturation of lipids in Escherichia coli (E. coli) and Acinetobacter baumannii (A. baumannii). When assigning sites of unsaturation, E. coli was found to contain all unsaturation elements at the same position relative to the terminal methyl carbon of the acyl chain; the first carbon participating in a site of unsaturation was consistently seven carbons along the acyl chain when counting carbons from the terminal methyl carbon. GPLs from A. baumannii exhibited more variability in locations of unsaturation. For GPLs containing sites of unsaturation in both acyl chains, an MS3 method was devised to assign sites to specific acyl chains.

Mass Spectrometry Based Approach for Organic Synthesis Monitoring.

Current mass spectrometry-based methodologies for synthetic organic reaction monitoring largely use electrospray ionization (ESI), or other related atmospheric pressure ionization-based approaches. Monitoring of complex, heterogeneous systems may be problematic because of sampling hardware limitations, and many relevant analytes (neutrals) exhibit poor ESI performance. An alternative monitoring strategy addressing this significant impasse is condensed phase membrane introduction mass spectrometry using liquid electron ionization (CP-MIMS-LEI). In CP-MIMS, a semipermeable silicone membrane selects hydrophobic neutral analytes, rejecting particulates and charged chemical components. Analytes partition through the membrane, and are then transported to the LEI interface for sequential nebulization, vaporization, and ionization. CP-MIMS and LEI are both ideal for continuous monitoring applications of hydrophobic neutral molecules. We demonstrate quantitative reaction monitoring of harsh, complex reaction mixtures (alkaline, acidic, heterogeneous) in protic and aprotic organic solvents. Also presented are solvent-membrane compatibility investigations and, in situ quantitative monitoring of catalytic oxidation and alkylation reactions.

Mass Spectrometry-Based Methodologies for Targeted and Untargeted Identification of Protein Covalent Adducts (Adductomics): Current Status and Challenges.

Protein covalent adducts formed upon exposure to reactive (mainly electrophilic) chemicals may lead to the development of a wide range of deleterious health outcomes. Therefore, the identification of protein covalent adducts constitutes a huge opportunity for a better understanding of events underlying diseases and for the development of biomarkers which may constitute effective tools for disease diagnosis/prognosis, for the application of personalized medicine approaches and for accurately assessing human exposure to chemical toxicants. The currently available mass spectrometry (MS)-based methodologies, are clearly the most suitable for the analysis of protein covalent modifications, providing accuracy, sensitivity, unbiased identification of the modified residue and conjugates along with quantitative information. However, despite the huge technological advances in MS instrumentation and bioinformatics tools, the identification of low abundant protein covalent adducts is still challenging. This review is aimed at summarizing the MS-based methodologies currently used for the identification of protein covalent adducts and the strategies developed to overcome the analytical challenges, involving not only sample pre-treatment procedures but also distinct MS and data analysis approaches.

Biofluid Metabolomics in Preterm Birth Research.

This article presents an account of the research carried out so far in the use of metabolomics to find biomarkers of preterm birth (PTB) in fetal, maternal, and newborn biofluids. Metabolomic studies have employed mainly nuclear magnetic resonance spectroscopy or mass spectrometry-based methodologies to analyze, on one hand, prenatal biofluids (amniotic fluid, maternal urine/maternal blood, cervicovaginal fluid) to identify predictive biomarkers of PTB, and on the other hand, biofluids collected at or after birth (amniotic fluid, umbilical cord blood, newborn urine, and newborn blood, maternal blood, or breast milk) to assess and follow up the health status of PTB babies. Besides advancing on the biochemical knowledge of PTB metabolism mainly during the in utero period and at birth, the work carried out has also helped to identify important requirements related to experimental design and analytical protocol that need to be addressed, if translation of these biomarkers to the clinic is to be envisaged. An outlook of possible future developments for the translation of laboratory results to the clinic is presented.

High resolution mass spectrometry-based methodologies for identification of Etravirine bioactivation to reactive metabolites: In vitro and in vivo approaches

Drug bioactivation to reactive metabolites capable of covalent adduct formation with bionucleophiles is a major cause of drug-induced adverse reactions. Therefore, elucidation of reactive metabolites is essential to unravel the toxicity mechanisms induced by drugs and thereby identify patient subgroups at higher risk.Etravirine (ETR) was the first second-generation Non-Nucleoside Reverse Transcriptase Inhibitor (NNRTI) to be approved, as a therapeutic option for HIV-infected patients who developed resistance to the first-generation NNRTIs. Additionally, ETR came into market aiming to overcome some adverse effects associated with the previously used efavirenz (neurotoxicity) and nevirapine (hepatotoxicity) therapies. Nonetheless, post-marketing reports of severe ETR-induced skin rash and hypersensitivity reactions have prompted the U.S. FDA to issue a safety alert on ETR. Taking into consideration that ETR usage may increase in the near future, due to the possible use of the drug for coinfection with malaria and HIV, the development of reliable prognostic tools for early risk/benefit estimations is urgent.In the current study, high resolution mass spectrometry-based methodologies were integrated with MS3 experiments for the identification of reactive ETR metabolites/adducts: 1) in vitro incubation of the drug with human and rat liver S9 fractions in the presence of Phase I and II co-factors, including glutathione, as a trapping bionucleophile; and 2) in vivo, using urine samples from HIV-infected patients on ETR therapy.We obtained evidence for multiple bioactivation pathways leading to the formation of covalent adducts with glutathione and N-acetyl-L-cysteine. These results suggest that similar reactions may occur with cysteine residues of proteins, supporting a role for ETR bioactivation in the onset of the toxic effects elicited by the drug. Additionally, ETR metabolites stemming from amine oxidation, with potential toxicological significance, were identified in vitro and in vivo. Also noteworthy is the fact that new metabolic conjugation pathways of glucuronide metabolites were demonstrated for the first time, raising questions about their potential toxicological implications. In conclusion, these results represent not only a contribution towards the elucidation of new metabolic pathways of drugs in general but also an important step towards the elucidation of potentially toxic ETR pathways, whose understanding may be crucial for reliable risk/benefit estimations of ETR-based regimens.

Quantitative study of zinc and metallothioneins in the human retina and RPE cells by mass spectrometry-based methodologies

The retina contains the highest concentration of zinc in the human eye and it is primarily associated with the retinal pigment epithelium (RPE). Metallothioneins (MTs) are the main cytosolic zinc-ion-binding proteins, exerting a tight control in the number of atoms of Zn-bound to the MTs related with their antioxidant and neuroprotective functions. In order to study the Zn-MT system in retina and RPE, we have implemented mass spectrometry (MS)-based technologies: two complementary element detection methodologies (HPLC- and laser ablation (LA)-ICP-MS) have been successfully employed to study metal content in the human eye as well as to perform speciation studies of Zn-MTs. First, Zn-elemental distribution was studied on cryogenic ocular sections by LA-ICP-MS. Quantitative images of Zn along RPE cell layer and the retina were obtained with a laser beam diameter of 25µm, showing a preferential distribution in the RPE. We carried out then the quantitative speciation of Zn, Fe, and Cu in the water-soluble protein fractions of RPE and retina to study their protein binding profile using HPLC-ICP-MS, where Zn is mainly associated to low molecular mass proteins (i.e., MTs). Finally, the effect of addition of different inductors, such as metal (i.e., 68ZnSO4), dexamethasone (DEX) and erythropoietin, was investigated in an in vitro cellular model of human RPE cells (HRPEsv), again using HPLC-ICP-MS in combination with stable isotopes and mathematical calculations based on isotope dilution and isotope pattern deconvolution. Exogenous Zn and DEX were found to increase MT proteins synthesis and exerted a stoichiometric transition in MT proteins in HRPEsv cells.

Systemic alterations in the metabolome of diabetic NOD mice delineate increased oxidative stress accompanied by reduced inflammation and hypertriglyceremia.

Nonobese diabetic (NOD) mice are a commonly used model of type 1 diabetes (T1D). However, not all animals will develop overt diabetes despite undergoing similar autoimmune insult. In this study, a comprehensive metabolomic approach, consisting of gas chromatography time-of-flight (GC-TOF) mass spectrometry (MS), ultra-high-performance liquid chromatography-accurate mass quadruple time-of-flight (UHPLC-qTOF) MS and targeted UHPLC-tandem mass spectrometry-based methodologies, was used to capture metabolic alterations in the metabolome and lipidome of plasma from NOD mice progressing or not progressing to T1D. Using this multi-platform approach, we identified >1,000 circulating lipids and metabolites in male and female progressor and nonprogressor animals (n = 71). Statistical and multivariate analyses were used to identify age- and sex-independent metabolic markers, which best differentiated metabolic profiles of progressors and nonprogressors. Key T1D-associated perturbations were related with 1) increases in oxidation products glucono-δ-lactone and galactonic acid and reductions in cysteine, methionine and threonic acid, suggesting increased oxidative stress; 2) reductions in circulating polyunsaturated fatty acids and lipid signaling mediators, most notably arachidonic acid (AA) and AA-derived eicosanoids, implying impaired states of systemic inflammation; 3) elevations in circulating triacylglyercides reflective of hypertriglyceridemia; and 4) reductions in major structural lipids, most notably lysophosphatidylcholines and phosphatidylcholines. Taken together, our results highlight the systemic perturbations that accompany a loss of glycemic control and development of overt T1D.

Applications of mass spectrometry for cellular lipid analysis.

Mass spectrometric analysis of cellular lipids is an enabling technology for lipidomics, which is a rapidly-developing research field. In this review, we briefly discuss the principles, advantages, and possible limitations of electrospray ionization (ESI) and matrix assisted laser desorption/ionization (MALDI) mass spectrometry-based methodologies for the analysis of lipid species. The applications of these methodologies to lipidomic research are also summarized.

Integrating meta-analysis of microarray data and targeted proteomics for biomarker identification: application in breast cancer.

The development of signature biomarkers has gained considerable attention in the past decade. Although the most well-known examples of biomarker panels stem from gene expression studies, proteomic panels are becoming more relevant, with the advent of targeted mass spectrometry-based methodologies. At the same time, the development of multigene prognostic classifiers for early stage breast cancer patients has resulted in a wealth of publicly available gene expression data from thousands of breast cancer specimens. In the present study, we integrated transcriptome and proteome-based platforms to identify genes and proteins related to patient survival. Candidate biomarker proteins have been identified in a previously generated breast cancer tissue extract proteome. A mass-spectrometry-based assay was then developed for the simultaneous quantification of these 20 proteins in breast cancer tissue extracts. We quantified the relative expression levels of the 20 potential biomarkers in a cohort of 96 tissue samples from patients with early stage breast cancer. We identified two proteins, KPNA2 and CDK1, which showed potential to discriminate between estrogen receptor positive patients of high and low risk of disease recurrence. The role of these proteins in breast cancer prognosis warrants further investigation.

Frontiers in Bioengineering Research

Over the last 25 years, the field of bioengineering has been revolutionized in both research and education. This has been “fueled” largely by the great advances in biology and medicine over the last few decades, and the significant investments made by the Whitaker Foundation. A new engineering discipline, “rooted” in biology, has emerged which represents a transformation from a discipline based on the traditional engineering sciences to one that integrates engineering with biology and medicine, an engineering discipline based on biology. Bioengineering has become a truly interdisciplinary and multidisciplinary field with much of the research efforts hypothesis driven and/or application driven, achieving a quantitative, systems-level understanding of the fundamental biological behavior of living cells and animals, and the translation of advanced biotechnologies to medicine.

Characterization of Electron Ionization Mass Spectral (EIMS) Fragmentation Patterns of Chloropropanol Esters of Palmitic Acid Using Isotope Labeling Technique

Chloropropanol (CP) esters are a class of thermally-induced toxicants that are mainly formed in refined edible oils. The structural diversity of these esters presents significant analytical challenges which have often been overcome through analysis of their corresponding free alcohols after a hydrolysis step. Mass spectrometry-based methodologies incorporating characteristic fragmentation patterns of particular isomers of CP esters greatly facilitates their identification. The electron ionization mass spectra (EIMS) of various isomers of synthetic and commercially available (13)C- and (2)H-labeled CP ester standards of palmitic (C16) and other short chain fatty acids (C3 to C10) were generated and analyzed using GC/MS. Short chain CP esters were synthesized by reacting their respective acid anhydrides with the corresponding 3-chloro- and 2-chloro- propanediols in addition to 1,3-dichloro- and 1,2-dichloropropanols. Five fragmentation pathways were identified. Four of the five pathways, such as α-cleavage, McLafferty rearrangement, α-H rearrangement and cyclic acyloxonium ion formation, were characteristic of CP mono- and diesters. The remaining pathway generating chloronium ion was found only in dichlorinated isomers. The proposed fragmentation pathways for the palmitic acid esters were confirmed through the use of (13)C- and (2)H-labeled CP ester standards of palmitic acid, and the generality of identified fragmentation patterns was confirmed through the identification of equivalent ions in the mass spectra of short chain fatty acids (C3 to C16). Characteristic ions that were identified in this study retaining the chlorine atom in their structures can be considered as potential markers for the presence of CP esters.

Isotope Labeling Studies on the Electron Impact Mass Spectral Fragmentation Patterns of Chloropropanol Acetates

Chloropropanol (CP) esters are part of an emerging group of process-induced toxicants that are considered as potential health hazards particularly in palm oil. Mass spectrometry-based methodologies for identification of CP esters in food are critical in overcoming the challenges associated with direct detection methods. In the present study, a convenient strategy was employed to generate all possible CP acetates through reacting acetic anhydride with either glycerol in the presence of a chloride source or the corresponding CPs, such as 3-chloro-, 1,3-dichloro-, 2-chloro-, and 1,2-dichloropropanols, allowing for the identification of the individual CP acetates and assignment of their mass spectral fragmentations. Mass spectral fragmentations were confirmed through the use of the isotopic signature of chlorine in addition to the isotope labeling experiments performed using isotopically labeled precursors, such as [¹³C-U₃] glycerol, [¹³C-U₄] acetic anhydride, [¹³C-2,2'] acetic anhydride, and [d₅] 3-monochloropropane-1,2-diol (3-MCPD) as reactants. Such studies have indicated that all CP esters can undergo two general fragmentations under electron impact (EI) conditions, one generating the acylium ion at m/z 45 and the other generating a chlorinated cyclic acyloxonium ion at m/z 135.6. Considering the fact that such ions can also be generated from any fatty acid containing CP esters after undergoing McLafferty rearrangement, the ion at m/z 135.6 can therefore be considered as a universal marker for the presence of CP esters undergoing EI fragmentation. Furthermore, these studies have also indicated the formation of ions characteristic of CP diesters, monoesters, and dichloro esters.

Chemical Tools for Temporally and Spatially Resolved Mass Spectrometry-Based Proteomics

Accurate measurements of the abundances, synthesis rates and degradation rates of cellular proteins are critical for understanding how cells and organisms respond to changes in their environments. Over the past two decades, there has been increasing interest in the use of mass spectrometry for proteomic analysis. In many systems, however, protein diversity as well as cell and tissue heterogeneity limit the usefulness of mass spectrometry-based proteomics. As a result, researchers have had difficulty in systematically identifying proteins expressed within specified time intervals, or low abundance proteins expressed in specific tissues or in a few cells in complex microbial systems. In this review, we present recently-developed tools and strategies that probe these two subsets of the proteome: proteins synthesized during well-defined time intervals--temporally resolved proteomics--and proteins expressed in predetermined cell types, cells or cellular compartments--spatially resolved proteomics--with a focus on chemical and biological mass spectrometry-based methodologies.

Molecular Characterization of Collagen Hydroxylysine O-Glycosylation by Mass Spectrometry: Current Status.

The most abundant proteins in vertebrates - the collagen family proteins - play structural and biological roles in the body. The predominant member, type I collagen, provides tissues and organs with structure and connectivity. This protein has several unique post-translational modifications that take place intra- and extra-cellularly. With growing evidence of the relevance of such post-translational modifications in health and disease, the biological significance of O-linked collagen glycosylation has recently drawn increased attention. However, several aspects of this unique modification - the requirement for prior lysyl hydroxylation as a substrate, involvement of at least two distinct glycosyl transferases, its involvement in intermolecular crosslinking - have made its molecular mapping and quantitative characterization challenging. Such characterization is obviously crucial for understanding its biological significance. Recent progress in mass spectrometry has provided an unprecedented opportunity for this type of analysis. This review summarizes recent advances in the area of O-glycosylation of fibrillar collagens and their characterization using state-of-the-art liquid chromatography-mass spectrometry-based methodologies, and perspectives on future research. The analytical characterization of collagen crosslinking and advanced glycation end-products are not addressed here.

Pathogen identifi cation using mass spectrometry in the clinical microbiology laboratory

Numerous microbes pose a significant threat in many environments, particularly so in the clinical setting where the most vulnerable patients are at high risk of infection. It is of prime importance to rapidly and accurately identify the responsible bacterial strains to appropriately disinfect contaminated areas and treat infected patients with upmost efficacy. In this regard, the recent development of mass spectrometry approaches for microbial identification has initiated a revolution in clinical microbiology laboratories. In this perspective article, Richard Drake and colleagues describe state-of-the-art mass spectrometry-based methodologies and instrumentation for microbial identification and give a perspective on future developments in the field. Richard Drake (Ph.D.) is newly appointed Professor and head of the Proteomic Center at the Medical University of South Carolina (Charleston, SC).