Peptide and protein identification by matrix-assisted laser desorption ionization (MALDI) and MALDI-post-source decay time-of-flight mass spectrometry

Identification of a 10-mer peptide from the death domain of MyD88 which attenuates inflammation and insulin resistance and improves glucose metabolism

Insulin resistance (IR) is the key pathophysiological cause of type 2 diabetes, and inflammation has been implicated in it. The death domain (DD) of the adaptor protein, MyD88 plays a crucial role in the transduction of TLR4-associated inflammatory signal. Herein, we have identified a 10-residue peptide (M10), from the DD of MyD88 which seems to be involved in Myddosome formation. We hypothesized that M10 could inhibit MyD88-dependent TLR4-signaling and might have effects on inflammation-associated IR. Intriguingly, 10-mer M10 showed oligomeric nature and reversible self-assembly property indicating the peptide's ability to recognize its own amino acid sequence. M10 inhibited LPS-induced nuclear translocation of NF-κB in L6 myotubes and also reduced LPS-induced IL-6 and TNF-α production in peritoneal macrophages of BALB/c mice. Remarkably, M10 inhibited IL-6 and TNF-α secretion in diabetic, db/db mice. Notably, M10 abrogated IR in insulin-resistant L6 myotubes, which was associated with an increase in glucose uptake and a decrease in Ser307-phosphorylation of IRS1, TNF-α-induced JNK activation and nuclear translocation of NF-κB in these cells. Alternate day dosing with M10 (10 and 20 mg/kg) for 30 days in db/db mice significantly lowered blood glucose and improved glucose intolerance after loading, 3.0 g/kg glucose orally. Furthermore, M10 increased insulin and adiponectin secretion in db/db mice. M10-induced glucose uptake in L6 myotubes involved the activation of PI3K/AKT/GLUT4 pathways. A scrambled M10-analog was mostly inactive. Overall, the results show the identification of a 10-mer peptide from the DD of MyD88 with anti-inflammatory and anti-diabetic properties, suggesting that targeting of TLR4-inflammatory pathway, could lead to the discovery of molecules against IR and diabetes.

Mass Spectrometry-Based Immunopeptidomics of Peptides Presented on Human Leukocyte Antigen Proteins

Human leukocyte antigen (HLA) proteins are a group of glycoproteins that are expressed at the cell surface, where they present peptides to T cells through physical interactions with T-cell receptors (TCRs). Hence, characterizing the set of peptides presented by HLA proteins, referred to hereafter as the immunopeptidome, is fundamental for neoantigen identification, immunotherapy, and vaccine development. As a result, different methods have been used over the years to identify peptides presented by HLA proteins, including competition assays, peptide microarrays, and yeast display systems. Nonetheless, over the last decade, mass spectrometry-based immunopeptidomics (MS-immunopeptidomics) has emerged as the gold-standard method for identifying peptides presented by HLA proteins. MS-immunopeptidomics enables the direct identification of the immunopeptidome in different tissues and cell types in different physiological and pathological states, for example, solid tumors or virally infected cells. Despite its advantages, it is still an experimentally and computationally challenging technique with different aspects that need to be considered before planning an MS-immunopeptidomics experiment, while conducting the experiment and with analyzing and interpreting the results. Hence, we aim in this chapter to provide an overview of this method and discuss different practical considerations at different stages starting from sample collection until data analysis. These points should aid different groups aiming at utilizing MS-immunopeptidomics, as well as, identifying future research directions to improve the method.

Detection of Short Peptides as Putative Biosignatures of Psychrophiles via Laser Desorption Mass Spectrometry

Studies of psychrophilic life on Earth provide chemical clues as to how extraterrestrial life could maintain viability in cryogenic environments. If living systems in ocean worlds (e.g., Enceladus) share a similar set of 3-mer and 4-mer peptides to the psychrophile Colwellia psychrerythraea on Earth, spaceflight technologies and analytical methods need to be developed to detect and sequence these putative biosignatures. We demonstrate that laser desorption mass spectrometry, as implemented by the CORALS spaceflight prototype instrument, enables the detection of protonated peptides, their dimers, and metal adducts. The addition of silicon nanoparticles promotes the ionization efficiency, improves mass resolving power and mass accuracies via reduction of metastable decay, and facilitates peptide de novo sequencing. The CORALS instrument, which integrates a pulsed UV laser source and an Orbitrap™ mass analyzer capable of ultrahigh mass resolving powers and mass accuracies, represents an emerging technology for planetary exploration and a pathfinder for advanced technique development for astrobiological objectives. Teaser: Current spaceflight prototype instrument proposed to visit ocean worlds can detect and sequence peptides that are found enriched in at least one strain of microbe surviving in subzero icy brines via silicon nanoparticle-assisted laser desorption analysis.

Functional properties of individual sub-domains of the fibrin(ogen) αC-domains

Background

Fibrinogen is a large polyfunctional plasma protein consisting of a number of structural and functional domains. Among them, two αC-domains, each formed by the amino acid residues Аα392-610, are involved in fibrin polymerization, activation of fibrinolysis, platelet aggregation, and interaction with different cell types. Previous study revealed that each fibrinogen αC-domain consists of the N-terminal and C-terminal sub-domains. The major objections of the present study were to test functional role of these sub-domains in the above mentioned processes.

Methods

To achieve these objections, we used specific proteases to prepare two truncated forms of fibrinogen, fibrinogen desAα505-610 and fibrinogen desAα414-610, missing their N-terminal and both N- and C-terminal sub-domains, respectively.

Results

Our study with these truncated forms using turbidity measurements and electron microscopy revealed that the N- and C-terminal subdomains both contribute to protofibril formation and their lateral aggregation into fibers during fibrin polymerization process. These two sub-domains also contributed to platelet aggregation with the N-terminal sub-domains playing a more significant role in this process. At the same time, the C-terminal sub-domains make the major contribution to the plasminogen activation process. Further, our experiments revealed that the C-terminal sub-domains are involved in endothelial cell viability and migration of cancer cells.

Conclusions

Thus, the results obtained establish the functional role of individual sub-domains of the αC-domains in fibrin polymerization, activation of fibrinolytic system, platelet aggregation, and cellular interactions.

General significance

The present study expands our understanding of the functional role of individual fibrinogen domains and their specific portions in various fibrin(ogen)-dependent processes.

Momomycin, an Antiproliferative Cryptic Metabolite from the Oxytetracycline Producer Streptomyces rimosus

Natural products provide an important source of pharmaceuticals and chemical tools. Traditionally, assessment of unexplored microbial phyla has led to new natural products. However, with every new microbe, the number of orphan biosynthetic gene clusters (BGC) grows. As such, the more difficult proposition is finding new molecules from well-studied strains. Herein, we targeted Streptomyces rimosus, the widely-used oxytetracycline producer, for the discovery of new natural products. Using MALDI-MS-guided high-throughput elicitor screening (HiTES), we mapped the global secondary metabolome of S. rimosus and structurally characterized products of three cryptic BGCs, including momomycin, an unusual cyclic peptide natural product with backbone modifications and several non-canonical amino acids. We elucidated important aspects of its biosynthesis and evaluated its bioactivity. Our studies showcase HiTES as an effective approach for unearthing new chemical matter from "drained" strains.

Unequivocal Identification of Aspartic Acid and isoAspartic Acid by MALDI-TOF/TOF: From Peptide Standards to a Therapeutic Antibody

Aspartic acid (Asp) to isoaspartic acid (isoAsp) isomerization in therapeutic monoclonal antibodies (mAbs) and other biotherapeutics is a critical quality attribute (CQA) that requires careful control and monitoring during the drug discovery and production processes. The unwanted formation of isoAsp within biotherapeutics and resultant structural changes in the peptide backbone may negatively impact the efficacy, potency, and safety of the molecule or become immunogenic, especially if the isomerization occurs within the mAb complementarity determining region (CDR). Herein we describe a MALDI-TOF/TOF mass spectrometry method that affords unequivocal identification of the presence and the exact position of the isoAsp residue(s) in peptide standards ranging in size from a tripeptide to a docosapeptide (22 residues). In general, the peptide bond immediately N-terminal to the isoAsp residue is more susceptible to MALDI-TOF/TOF fragmentation than its unmodified counterpart. In some of the peptides evaluated in this study, fragmentation of the peptide bond C-terminal to the isoAsp residue (the aspartate effect) is also enhanced when compared to the control. Relative quantification by MALDI-TOF/TOF of this chemical modification is dependent upon a successful reversed-phase HPLC (rpHPLC) separation of the control and modified peptides. This method has also been validated on a therapeutic mAb that contains a well-documented isoAsp residue in the heavy chain CDR3 after forced degradation. Moreover, we also demonstrate that higher energy C-trap dissociation of only the singly charged species, and not the multiply charged form, of the isoAsp containing peptide, separated by rpHPLC, results in LC-MS/MS fragmentation that is highly consistent to that of MALDI-TOF/TOF.

Discovery of a Cryptic Depsipeptide from Streptomyces ghanaensis via MALDI-MS-Guided High-Throughput Elicitor Screening

Microbial genomes harbor an abundance of biosynthetic gene clusters, but most are expressed at low levels and need to be activated for characterization of their cognate natural products. In this work, we report the combination of high-throughput elicitor screening (HiTES) with matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) for the rapid identification of cryptic peptide natural products. Application to Streptomyces ghanaensis identified amygdalin as an elicitor of a novel non-ribosomal peptide, which we term cinnapeptin. Complete structural elucidation revealed cinnapeptin as a cyclic depsipeptide with an unusual 2-methyl-cinnamoyl group. Insights into its biosynthesis were provided by whole genome sequencing and gene deletion studies, while bioactivity assays showed antimicrobial activity against Gram-positive bacteria and fission yeast. MALDI-HiTES is a broadly applicable tool for the discovery of cryptic peptides encoded in microbial genomes.

Mass Spectrometric (MS) Analysis of Proteins and Peptides

The human genome is sequenced and comprised of ~30,000 genes, making humans just a little bit more complicated than worms or flies. However, complexity of humans is given by proteins that these genes code for because one gene can produce many proteins mostly through alternative splicing and tissue-dependent expression of particular proteins. In addition, post-translational modifications (PTMs) in proteins greatly increase the number of gene products or protein isoforms. Furthermore, stable and transient interactions between proteins, protein isoforms/proteoforms and PTM-ed proteins (protein-protein interactions, PPI) add yet another level of complexity in humans and other organisms. In the past, all of these proteins were analyzed one at the time. Currently, they are analyzed by a less tedious method: mass spectrometry (MS) for two reasons: 1) because of the complexity of proteins, protein PTMs and PPIs and 2) because MS is the only method that can keep up with such a complex array of features. Here, we discuss the applications of mass spectrometry in protein analysis.

Evaluation of Sibling and Twin Fragment Ions Improves the Structural Characterization of Proteins by Top-Down MALDI In-Source Decay Mass Spectrometry

Comprehensive determination of primary sequence and identification of post-translational modifications (PTMs) are key elements in protein structural analysis. Various mass spectrometry (MS) based fragmentation techniques are powerful approaches for mapping both the amino acid sequence and PTMs; one of these techniques is matrix-assisted laser desorption/ionization (MALDI), combined with in-source decay (ISD) fragmentation and Fourier-transform ion cyclotron resonance (FT-ICR) MS. MALDI-ISD MS protein analysis involves only minimal sample preparation and does not require spectral deconvolution. The resulting MALDI-ISD MS data is complementary to electrospray ionization-based MS/MS sequencing readouts, providing knowledge on the types of fragment ions is available. In this study, we evaluate the isotopic distributions of z′ ions in protein top-down MALDI-ISD FT-ICR mass spectra and show why these distributions can deviate from theoretical profiles as a result of co-occurring and isomeric z and y-NH₃ ions. Two synthetic peptides, containing either normal or deuterated alanine residues, were used to confirm the presence and unravel the identity of isomeric z and y-NH₃ fragment ions (“twins”). Furthermore, two reducing MALDI matrices, namely 1,5-diaminonaphthalene and N-phenyl-p-phenylenediamine were applied that yield ISD mass spectra with different fragment ion distributions. This study demonstrates that the relative abundance of isomeric z and y-NH₃ ions requires consideration for accurate and confident assignments of z′ ions in MALDI-ISD FT-ICR mass spectra.

Impacts of glycation and transglutaminase-catalyzed glycosylation with glucosamine on the conformational structure and allergenicity of bovine β-lactoglobulin

β-Lactoglobulin (β-LG) is recognized as the major milk allergen. In this study, the effects of transglutaminase (TGase) and glucosamine (GlcN)-catalyzed glycosylation and glycation on the conformational structure and allergenicity of β-LG were investigated. The formations of cross-linked peptides were demonstrated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), and GlcN-conjugated modification was identified using matrix-assisted laser desorption ionization-time of flight-mass spectrometry (MALDI-TOF-MS). Structural analysis revealed that glycosylation and glycation of β-LG induced unfolding of the primary protein structure followed by a loss of the secondary structure. As revealed by circular dichroism (CD) spectroscopy, glycosylated β-LG exhibited the highest increase in the β-sheets from 32.6% to 40.4% (25 °C) and 44.2% (37 °C), and the percentage of α-helices decreased from 17.7% to 14.4% (25 °C) and 12.3% (37 °C), respectively. The tertiary and quaternary structures of β-LG also changed significantly during glycosylation and glycation, along with reduced free amino groups and variation in surface hydrophobicity. Immunoblotting and indirect enzyme-linked immuno sorbent assay (ELISA) analyses demonstrated that the lowest IgG- and IgE-binding capacities of β-LG were obtained following glycosylation at 37 °C, which were 52.7% and 56.3% lower than that of the native protein, respectively. The reduction in the antigenicity and potential allergenicity of glycosylated β-LG was more pronounced compared to TGase treated- and glycated β-LG, which correlated well with the structural changes. These results suggest that TGase-catalyzed glycosylation has more potential compared to glycation for mitigating the allergenic potential of milk products.

Principles of hydrogen radical mediated peptide/protein fragmentation during matrix-assisted laser desorption/ionization mass spectrometry

Matrix-assisted laser desorption/ionization in-source decay (MALDI-ISD) is a very easy way to obtain large sequence tags and, thereby, reliable identification of peptides and proteins. Recently discovered new matrices have enhanced the MALDI-ISD yield and opened new research avenues. The use of reducing and oxidizing matrices for MALDI-ISD of peptides and proteins favors the production of fragmentation pathways involving "hydrogen-abundant" and "hydrogen-deficient" radical precursors, respectively. Since an oxidizing matrix provides information on peptide/protein sequences complementary to that obtained with a reducing matrix, MALDI-ISD employing both reducing and oxidizing matrices is a potentially useful strategy for de novo peptide sequencing. Moreover, a pseudo-MS(3) method provides sequence information about N- and C-terminus extremities in proteins and allows N- and C-terminal side fragments to be discriminated within the complex MALDI-ISD mass spectrum. The combination of high mass resolution of a Fourier transform-ion cyclotron resonance (FTICR) analyzer and the software suitable for MALDI-ISD facilitates the interpretation of MALDI-ISD mass spectra. A deeper understanding of the MALDI-ISD process is necessary to fully exploit this method. Thus, this review focuses first on the mechanisms underlying MALDI-ISD processes, followed by a discussion of MALDI-ISD applications in the field of proteomics. © 2014 Wiley Periodicals, Inc., Mass Spec Rev 35:535-556, 2016.

Doping He droplets by laser ablation with a pulsed supersonic jet source

Laser ablation offers the possibility to study a rich number of atoms, molecules, and clusters in the gas phase. By attaching laser ablated materials to helium nanodroplets, one can gain highly resolved spectra of isolated species in a cold, weakly perturbed system. Here, we present a new setup for doping pulsed helium nanodroplet beams by means of laser ablation. In comparison to more well-established techniques using a continuous nozzle, pulsed nozzles show significant differences in the doping efficiency depending on certain experimental parameters (e.g., position of the ablation plume with respect to the droplet formation, nozzle design, and expansion conditions). In particular, we demonstrate that when the ablation region overlaps with the droplet formation region, one also creates a supersonic beam of helium atoms seeded with the sample material. The processes are characterized using a surface ionization detector. The overall doping signal is compared to that of conventional oven cell doping showing very similar dependence on helium stagnation conditions, indicating a comparable doping process. Finally, the ablated material was spectroscopically studied via laser induced fluorescence.

Organic–inorganic binary mixture matrix for comprehensive laser-desorption ionization mass spectrometric analysis and imaging of medium-size molecules including phospholipids, glycerolipids, and oligosaccharides

A binary matrix of DHB and Fe₃O₄ NPs provides broad coverage for medium size metabolites.

Liquid chromatography tandem mass spectrometry in the clinical laboratory

Clinical laboratory medicine has seen the introduction and evolution of liquid chromatography tandem mass spectrometry in routine clinical laboratories over the last 10–15 years. There still exists a wide diversity of assays from very esoteric and highly specialist manual assays to more simplified kit-based assays. The technology is not static as manufacturers are continually making improvements. Mass spectrometry is now commonly used in several areas of diagnostics including therapeutic drug monitoring, toxicology, endocrinology, paediatrics and microbiology. Some of the most high throughput analyses or common analytes include vitamin D, immunosuppressant monitoring, androgen measurement and newborn screening. It also offers flexibility for the measurement of analytes in a variety of different matrices which would prove difficult with immunoassays. Unlike immunoassays or high-pressure liquid chromatography assays using ultraviolet or fluorescence detection, mass spectrometry offers better specificity and reduced interferences if attention is paid to potential isobaric compounds. Furthermore, multiplexing, which enables multiple analytes to be measured with the same volume of serum is advantageous, and the requirement for large sample volumes is decreasing as instrument sensitivity increases. There are many emerging applications in the literature. Using mass spectrometry to identify novel isoforms or modified peptides is possible as is quantification of proteins and peptides, with or without protein digests. Future developments by the manufacturers may also include mechanisms to improve the throughput of samples and strategies to decrease the level of skill required by the operators.

Overview of peptide and protein analysis by mass spectrometry

Mass spectrometry is an indispensable tool for peptide and protein analysis owing to its speed, sensitivity, and versatility. It can be used to determine amino acid sequences of peptides, and to characterize a wide variety of post-translational modifications such as phosphorylation and glycosylation. Mass spectrometry can also be used to determine absolute and relative protein quantities, and can identify and quantify thousands of proteins from complex samples, which makes it an extremely powerful tool for systems biology studies. The main goals of this unit are to familiarize peptide and protein chemists and biologists with the types of mass spectrometers that are appropriate for the majority of their analytical needs, to describe the kinds of experiments that can be performed with these instruments on a routine basis, and to discuss the kinds of information that these experiments provide.

New approach for pseudo-MS(3) analysis of peptides and proteins via MALDI in-source decay using radical recombination with 1,5-diaminonaphthalene

Matrix-assisted laser desorption ionization in-source decay (MALDI-ISD) is a useful method for top-down sequencing of proteins and preferentially produces the c'/z(•) fragment pair. Subsequently, radical z(•) fragments undergo a variety of radical reactions. This work is focused on the chemical properties of the 1,5-diaminonaphthalene (1,5-DAN) adducts on z fragment ions (zn*), which are abundant in MALDI-ISD spectra. Postsource decay (PSD) of the zn* fragments resulted in specific peptide bond cleavage adjacent to the binding site of 1,5-DAN, leading to the preferential formation of y'n-1 fragments. The dominant loss of an amino acid with 1,5-DAN from zn* can be used in pseudo-MS(3) mode to identify the C-terminal side fragments from a complex MALDI-ISD spectrum or to determine missed cleavage residues using MALDI-ISD. Although the N-Cα bond at the N-terminal side of Pro is not cleaved by MALDI-ISD, pseudo-MS(3) via zn* can confirm the presence of a Pro residue.

Layer-by-layer thin film of reduced graphene oxide and gold nanoparticles as an effective sample plate in laser-induced desorption/ionization mass spectrometry

This work demonstrated a simple platform for rapid and effective surface-assisted laser desorption/ionization time-of-flight mass spectrometry (SALDI-TOF MS) measurements based on the layer structure of reduced graphene oxide (rGO) and gold nanoparticles. A multi-layer thin film was fabricated by alternate layer-by-layer depositions of rGO and gold nanoparticles (LBL rGO/AuNP). The flat and clean two-dimensional film was served as the sample plate and also functioned as the matrix in SALDI-TOF MS. By simply one-step deposition of analytes onto the LBL rGO/AuNP sample plate, the MS measurements of various homogeneous samples were ready to execute. The optimization of MS signal was reached by the variation of the layer numbers of rGO and gold nanoparticles. Also, the small molecules including amino acids, carbohydrates and peptides were successfully analyzed in SALDI-TOF MS using the LBL rGO/AuNP sample plate. The results showed that the signal intensity, S N(-1) ratio and reproducibility of SALDI-TOF spectra have been significantly improved in comparison to the uses of gold nanoparticles or α-cyano-4-hydroxy-cinnamic acid (CHCA) as the assisted matrixes. Taking the advantages of the unique properties of rGO and gold nanoparticles, the ready-to-use MS sample plate, which could absorb and dissipate laser energy to analytes quite efficiently and homogeneously, has shown great commercial potentials for MS applications.

Rapid estimation of the energy charge from cell lysates using matrix-assisted laser desorption/ionization mass spectrometry: role of in-source fragmentation

Nucleotides are key players in the central energy metabolism of cells. Here we show how to estimate the energy charge from cell lysates by direct negative ion matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) using 9-aminoacridine as matrix. We found a high level of in-source decay of all the phosphorylated nucleotides, with some of them producing considerable amounts of adenosine-5'-diphosphate (ADP) fragment ions. We investigated the behavior of adenosine-5'-monophosphate (AMP), ADP, and adenosine-5'-triphosphate (ATP) as well as the cofactors coenzyme A (CoA) and acetyl-coenzyme A (ACoA) and nicotinamide adenine dinucleotides (NAD⁺ and NADH) in detail. In-source decay of these compounds depends strongly on the applied laser power and on the extraction pulse delay. At standard instrument settings, the 9-aminoacridine (9-AA) matrix resulted in a much higher in-source decay compared with 2,4,6-trihydroxyacetophenone (2,4,6-THAP). By adding ¹³C-labeled ATP to a cell lysate, we were able to determine the degree of in-source decay during an experiment. Analyzing a cell extract of the monocytic cell line THP-1 with [¹³C]ATP as internal standard, we were able to obtain values for the energy charge that were similar to those determined by a reference liquid chromatography electrospray ionization coupled to mass spectrometry (LC-ESI-MS) method.

Mass spectrometry imaging with high resolution in mass and space

Mass spectrometry (MS) imaging links molecular information and the spatial distribution of analytes within a sample. In contrast to most histochemical techniques, mass spectrometry imaging can differentiate molecular modifications and does not require labeling of targeted compounds. We have recently introduced the first mass spectrometry imaging method that provides highly specific molecular information (high resolution and accuracy in mass) at cellular dimensions (high resolution in space). This method is based on a matrix-assisted laser desorption/ionization (MALDI) imaging source working at atmospheric pressure which is coupled to an orbital trapping mass spectrometer. Here, we present a number of application examples and demonstrate the benefit of ‘mass spectrometry imaging with high resolution in mass and space.’ Phospholipids, peptides and drug compounds were imaged in a number of tissue samples at a spatial resolution of 5–10 μm. Proteins were analyzed after on-tissue tryptic digestion at 50-μm resolution. Additional applications include the analysis of single cells and of human lung carcinoma tissue as well as the first MALDI imaging measurement of tissue at 3 μm pixel size. MS image analysis for all these experiments showed excellent correlation with histological staining evaluation. The high mass resolution (R = 30,000) and mass accuracy (typically 1 ppm) proved to be essential for specific image generation and reliable identification of analytes in tissue samples. The ability to combine the required high-quality mass analysis with spatial resolution in the range of single cells is a unique feature of our method. With that, it has the potential to supplement classical histochemical protocols and to provide new insights about molecular processes on the cellular level.

Protein glycation in diabetes as determined by mass spectrometry

Diabetes is a common endocrine disorder characterized by hyperglycemia leading to nonenzymatic glycation of proteins, responsible for chronic complications. The development of mass spectrometric techniques able to give highly specific and reliable results in proteome field is of wide interest for physicians, giving them new tools to monitor the disease progression and the possible complications related to diabetes, as well as the effectiveness of therapeutic treatments. This paper reports and discusses some of the data pertaining protein glycation in diabetic subjects obtained by matrix-assisted laser desorption ionization (MALDI) mass spectrometry (MS). The preliminary studies carried out by in vitro protein glycation experiments show clear differences in molecular weight of glycated and unglycated proteins. Then, the attention was focused on plasma proteins human serum albumin (HSA) and immunoglobulin G (IgG). Enzymatic degradation products of in vitro glycated HSA were studied in order to simulate the in vivo enzymatic digestion of glycated species by the immunological system leading to the highly reactive advanced glycation end-products (AGEs) peptides. Further studies led to the evaluation of glycated Apo A-I and glycated haemoglobin levels. A different MALDI approach was employed for the identification of markers of disease in urine samples of healthy, diabetic, nephropathic, and diabetic-nephropathic subjects.

Peptide backbone fragmentation initiated by side-chain loss at cysteine residue in matrix-assisted laser desorption/ionization in-source decay mass spectrometry

Matrix-assisted laser desorption/ionization in-source decay (MALDI-ISD) is initiated by hydrogen transfer from matrix molecules to the carbonyl oxygen of peptide backbone with subsequent radical-induced cleavage leading to c'/z• fragments pair. MALDI-ISD is a very powerful method to obtain long sequence tags from proteins or to do de novo sequencing of peptides. Besides classical fragmentation, MALDI-ISD also shows specific fragments for which the mechanism of formation enlightened the MALDI-ISD process. In this study, the MALDI-ISD mechanism is reviewed, and a specific mechanism is studied in details: the N-terminal side of Cys residue (Xxx-Cys) is described to promote the generation of c' and w fragments in MALDI-ISD. Our data suggest that for sequences containing Xxx-Cys motifs, the N-Cα bond cleavage occurs following the hydrogen attachment to the thiol group of Cys side-chain. The c•/w fragments pair is formed by side-chain loss of the Cys residue with subsequent radical-induced cleavage at the N-Cα bond located at the left side (N-terminal direction) of the Cys residue. This fragmentation pathway preferentially occurs at free Cys residue and is suppressed when the cysteines are involved in disulfide bonds. Hydrogen attachment to alkylated Cys residues using iodoacetamide gives free Cys residue by the loss of •CH2CONH2 radical. The presence of alkylated Cys residue also suppress the formation of c•/w fragments pair via the (Cβ)-centered radical, whereas w fragment is still observed as intense signal. In this case, the z• fragment formed by hydrogen attachment of carbonyl oxygen followed side-chain loss at alkylated Cys leads to a w fragment. Hydrogen attachment on peptide backbone and side-chain of Cys residue occurs therefore competitively during MALDI-ISD process.

Commercial silicon-on-insulator (SOI) wafers as a versatile substrate for laser desorption/ionization mass spectrometry

We report here that a commercial silicon-on-insulator (SOI) wafer offers an opportunity for laser desorption/ionization (LDI) of peptide molecules, which occurs directly from its flat surface without requiring special surface preparation. The LDI-on-SOI exhibits intact ionization of peptides with a good detection limit of lower than 20 fmol, of which the mass range is demonstrated up to insulin with citric acid additives. The LDI process most likely arises from laser-induced surface heating promoted by two-dimensional thermal confinement in the thin Si surface layer of the SOI wafer. As a consequence of the thermal process, the LDI-on-SOI method is also capable of creating post-source decay (PSD) of the resulting peptide LDI ions, which is suitable for peptide sequencing using conventional TOF/TOF mass spectrometry.

Introduction to mass spectrometry-based proteomics

Mass spectrometry has been widely applied to study biomolecules and one rapidly developing field is the global analysis of proteins, proteomics. Understanding and handling mass spectrometry data is a multifaceted task that requires many decisions to be made to get the most comprehensive information from an experiment. Later chapters in this book deal in-depth with various aspects of the process and how different tools can be applied to the many analytical challenges. This introductory chapter is intended as a basic introduction to mass spectrometry (MS)-based proteomics to set the scene for newcomers and give pointers to reference material. There are many applications of mass spectrometry in proteomics and each application is associated with some analytical choices, instrumental limitations and data processing steps that depend on the aim of the study and means of conducting it. Different aspects of the proteome can be explored by choosing the right combination of sample preparation, MS instrumentation and data processing. This chapter gives an outline for some of these commonly used setups and some of the key concepts, many of which are explored in greater depth in later chapters.

N-(1-naphthyl) ethylenediamine dinitrate: a new matrix for negative ion MALDI-TOF MS analysis of small molecules

An organic salt, N-(1-naphthyl) ethylenediamine dinitrate (NEDN), with rationally designed properties of a strong UV absorbing chromophore, hydrogen binding and nitrate anion donors, has been employed as a matrix to analyze small molecules (m/z < 1000) such as oligosaccharides, peptides, metabolites and explosives using negative ion matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). Compared with conventional matrixes such as α-cyano-4-hydroxycinnamic acid (CCA) and 2,5-dihydroxybenzoic acid (DHB), NEDN provides a significant improvement in detection sensitivity and yields very few matrix-associated fragment and cluster ions interfering with MS analysis. For low-molecular-weight saccharides, the lowest detection limit achieved ranges from 500 amol to 5 pmol, depending on the molecular weight and the structure of the analytes. Additionally, the mass spectra in the lower mass range (m/z < 200) consist of only nitrate and nitric acid cluster ions, making the matrix particularly useful for structural identification of oligosaccharides by post-source decay (PSD) MALDI-MS. Such a characteristic is illustrated by using maltoheptaose as a model system. This work demonstrates that NEDN is a novel negative ion-mode matrix for MALDI-MS analysis of small molecules with nitrate anion attachment.

Matrix effect on in-source decay products of peptides in matrix-assisted laser desorption/ionization

MALDI-ISD of peptides were studied using several salicylic acid derivatives, 2,5-dihydroxybenzoic acid (2,5-DHB), 5-aminosalicylic acid (5-ASA), 5-formylsalicylic acid (5-FSA), and 5-nitrosalicylic acid (5-NSA) as matrices. The difference in the nature of the functional group at the 5-position in the salicylic acid derivatives can dramatically affect the ISD products. The use of 2,5-DHB and 5-ASA leads to "hydrogen-abundant" peptide radicals and subsequent radical-induced N-Cα bonds cleavage. N-Cα bond cleavage gave a c'/z (·) fragment pair and radical z (·)-series fragments gain a hydrogen radical or react with a matrix radical. In contrast, the use of 5-NSA resulted in the production of a "hydrogen-deficient" peptide radical that contained a radical site on the amide nitrogen in the peptide backbone. Subsequently, the radical site on the amide nitrogen induces Cα-C bond dissociation, leading to a (·)/x fragment pair. The a (·)-series ions undergo further hydrogen abstraction to form a-series ions after Cα-C bond cleavage. Since the Pro residue does not contain a nitrogen-centered radical site, Cα-C bond cleavage does not occur. Alternatively, the specific cleavage of CO-N bonds leads to a b (·)/y fragment pair at Xxx-Pro which occurs via hydrogen abstraction from the Cα-H in the Pro residue. The use of 5-FSA generated both a (·)/x- and c'/z (·)-series fragment pairs. An oxidizing matrix provides useful complementary information in MALDI-ISD compared to a reducing matrix for the analysis of amino acid sequencing and site localization in cases of phosphopeptides. MALDI-ISD, when used in conjunction with both reducing and oxidizing matrices is a potentially useful method for de novo peptide sequencing.

Laser-induced thermal desorption facilitates postsource decay of peptide ions

We investigated the thermal mechanism involved in laser desorption/ionization (LDI) of thermally labile molecules from the flat surfaces of amorphous Si (a-Si) and crystalline Si (c-Si). a-Si was selected for this study because of its thermal property, such as low thermal conductivity; thus, it was predicted to be highly susceptible to laser-induced surface heating. By virtue of lack of surface nanostructures, the flat surfaces offer a simple model system to focus on the thermal mechanism, avoiding other effects, including possible non-thermal contributions that can arise from the physical existence of surface nanostructures. For the energetics study, the internal energies of substituted benzylpyridinium ions produced by LDI on the bare and coated surfaces of a-Si and c-Si were obtained using the survival yield method. The results, including LDI thresholds, ion yields, and internal energies all suggested that the LDI mechanism would be indeed thermal, which is most likely promoted by thermal desorption caused by laser-induced surface heating. In addition, the LDI process driven by laser-induced thermal desorption (LITD) was also found to be capable of depositing an excessive internal energy in resulting LDI ions, which underwent a dissociation. It exhibited the essentially same features as in postsource decay (PSD) in MALDI-TOF/TOF mass spectrometry. We report that the LDI process by LITD offers not only a way of intact ionization but also a facile means for PSD of peptide ions, which this work demonstrates is well suited to peptide sequencing using TOF/TOF mass spectrometry.

Fragmentation processes of hydrogen-deficient peptide radicals in matrix-assisted laser desorption/ionization in-source decay mass spectrometry

The mechanism of in-source decay (ISD) in matrix-assisted laser desorption/ionization (MALDI) has been described. The MALDI-ISD with an oxidizing matrix is initiated by hydrogen abstraction from peptides to matrix molecules, leading to hydrogen-deficient peptide radicals. Subsequently, the C(α)-C and C(α)-H bonds are cleaved, forming the a•/x fragment pair and [M-2H], respectively. Those reactions competitively occur during MALDI-ISD processes. Our results suggest that the C(α)-H bond cleavage to form [M-2H] was induced by collisions between hydrogen-deficient peptide radicals and matrix molecules in the MALDI plume. In contrast, the C(α)-C bond cleavages occur via a unimolecular dissociation process and independently of the collision rate in the MALDI plume. The formation mechanism of the a-, b-, and d-series fragments are also described. We report 2,5-bis(2-hydroxyethoxy)-7,7,8,8-tetracyanoquinodimethane (bisHE-TCNQ), being known as an organic semiconductor and an electron acceptor, as a novel suitable matrix for the MALDI-ISD of peptides via hydrogen abstraction.

Production of reliable MALDI spectra with quality threshold clustering of replicates

We present the first application of the quality threshold (QT) clustering algorithm to mass spectrometry (MS) data. The unique abilities of QT clustering to yield precision nodes that are commensurate with the mass measurement precision of the instrument are exploited to generate a consensus spectrum out of multiple replicate spectra. The spectral dot product and confidence intervals are used as a tool for evaluating the similarity and reproducibility between the consensus and replicates. The method is equally applicable to high and low resolution measurements. This paper demonstrates applications to linear spectra from a matrix assisted laser desorption ionization (MALDI) time of flight (TOF) instrument as well as peptide fragmentation data obtained from a TOF/TOF after unimolecular decomposition. The advantages of clustering to mitigate the inherent precision the shortcomings of MALDI data are discussed.

Native mass spectrometry as a tool in structural biology

Native mass spectrometry (native MS) gives information about the composition, topological arrangements, dynamics, and structural properties of protein complexes. The mass range is principally unlimited and highly dynamic, allowing the detection of small subunits and large complexes within the same measurement. The amount of protein needed for an analysis is, compared to most other structural biology methods, very low. This unit provides an introduction to native MS. It starts with an explanation of the basic method and details on how to measure intact proteins and protein complexes, and continues with the study of dynamics and complex stability in the gas phase. The final section discusses the most recent extension to the native MS field, ion mobility, which allows the direct assessment of the structural properties of the complexes of interest.

Overview of peptide and protein analysis by mass spectrometry

Mass spectrometry is an indispensable tool for peptide and protein analysis owing to its speed, sensitivity, and versatility. It can be used to determine amino acid sequences of peptides, and to characterize a wide variety of post-translational modifications such as phosphorylation and glycosylation. Mass spectrometry can also be used to determine absolute and relative protein quantities, and can identify and quantify thousands of proteins from complex samples, which makes it an extremely powerful tool for systems biology studies. The main goals of this unit are to familiarize peptide and protein chemists and biologists with the types of mass spectrometers that are appropriate for the majority of their analytical needs, to describe the kinds of experiments that can be performed with these instruments on a routine basis, and to discuss the kinds of information that these experiments provide.

Azo-group reduction during the matrix-assisted laser desorption/ionization process in the presence of 2,5-dihydroxybenzoic acid

Some time ago, we published an announcement that the azo group that closes model cyclic peptides is often reduced in matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS) in the presence of 2,5-dihydroxybenzoic acid (2,5-DHB) as the matrix. In this work, we demonstrate that these peptides are ionized in all DHB matrix isomers, although threshold ionization laser energies as well as the reduction ratios differ in each matrix. Using a NALDI plate, we confirmed that their reduction depends on the presence of DHB matrix and that the hydrogen atoms participating in the reaction come from the DHB matrix hydroxyl group. We show that the reduction ratio is affected by the overall covalent structure of the peptide, by the presence of a free carboxyl group in DHB matrix, by the mutual position of the hydroxyl and carboxyl groups, as well as the laser beam intensity. Based on these results, it can be concluded that the azo-group reduction in cyclic peptides is a very complex process and we are far from fully understanding its nature. We hope that our experimental results will help to shed some light on the MALDI process that still remains mysterious in some of its aspects.

Reduced graphene oxide films used as matrix of MALDI-TOF-MS for detection of octachlorodibenzo-p-dioxin

A reduced graphene oxide (rGO) film was used as the matrix in the matrix-assisted laser desorption/ionization time-of-flight mass spectroscopy (MALDI-TOF-MS) for the detection of octachlorodibenzo-p-dioxin (OCDD) with a detection weight as low as 500 pg.

MALDI-TOF mass spectrometry approaches to the characterisation of insect neuropeptides

The diversity of insect neuropeptides coupled with the limitations from the small size of the insects themselves combine to make positive identification through peptide sequencing a highly challenging task. The advent of the "soft-ionisation" techniques of MALDI-TOF and electrospray (ESI)-Q-TOF mass spectrometry, coupled with the additional information from insect genome projects have revolutionised the characterisation of insect neuropeptides, such that sequences can now be obtained from just a few cells, where before thousands of insects had to be laboriously dissected, extracted and purified. Some of the procedures that are now used to identify these peptides are described here. Once the neuropeptides have been identified, it then becomes possible to use this knowledge to define physiological functionality.

Matrix vapor deposition/recrystallization and dedicated spray preparation for high-resolution scanning microprobe matrix-assisted laser desorption/ionization imaging mass spectrometry (SMALDI-MS) of tissue and single cells

Matrix preparation techniques such as air spraying or vapor deposition were investigated with respect to lateral migration, integration of analyte into matrix crystals and achievable lateral resolution for the purpose of high-resolution biological imaging. The accessible mass range was found to be beyond 5000 u with sufficient analytical sensitivity. Gas-assisted spraying methods (using oxygen-free gases) provide a good compromise between crystal integration of analyte and analyte migration within the sample. Controlling preparational parameters with this method, however, is difficult. Separation of the preparation procedure into two steps, instead, leads to an improved control of migration and incorporation. The first step is a dry vapor deposition of matrix onto the investigated sample. In a second step, incorporation of analyte into the matrix crystal is enhanced by a controlled recrystallization of matrix in a saturated water atmosphere. With this latter method an effective analytical resolution of 2 microm in the x and y direction was achieved for scanning microprobe matrix-assisted laser desorption/ionization imaging mass spectrometry (SMALDI-MS). Cultured A-498 cells of human renal carcinoma were successfully investigated by high-resolution MALDI imaging using the new preparation techniques.

Wavelength Dependence On The Level Of Post-Source Metastable Ion Decay Observed In Infrared Matrix-Assisted Laser Desorption Ionization

The levels of post-source metastable ion decay (PSD) observed in several peptides and proteins ionized by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI TOF-MS) are measured utilizing both infrared (IR) and ultraviolet (UV) desorption wavelengths. A gridless deceleration ion optic is employed to temporally separate stable analyte ions from analyte metastable neutral and ion fragments. Comparisons of the extent of PSD that is observed in UV-MALDI at 337 nm and IR-MALDI at multiple wavelengths between 2.8 and 3.0 mum are made using the same matrices and analytes. The amount of PSD observed using IR-MALDI was found to be highly dependent on the specific IR wavelength (2.8-3.0 mum) employed for desorption. IR wavelengths shorter than 2.86 mum tended to produce higher levels of PSD, while longer IR wavelengths typically produced significantly less PSD when using a number of common MALDI matrices. Relative PSD levels are quantified by determining the percentage of the neutral fragment signal intensity to the intensity of the stable singly protonated molecular species observed in decelerated MALDI spectra. These studies suggest that an analyte ion activation pathway leading to significant PSD in IR-MALDI may proceed by way of vibrational excitation of the analyte molecules during the desorption event.

From large analogical instruments to small digital black boxes: 40 years of progress in mass spectrometry and its role in proteomics. Part II 1985-2000

This is the continuation of a personal retrospective on the developments that since 1965 have given shape to Mass Spectrometry (MS) and taken it from a position of simply playing a role in Protein Chemistry to becoming an indispensable tool in Proteomics, all within a 40-year span. Part I covered the period from 1965 to 1984. This second part reviews the Mass Spectrometry timeline of events from 1985 to 2000, stopping at various time points where MS made significant contributions to protein chemistry or where the development of new instrumentation for MS represented a major advance for peptide and protein work. Major highlights in the field and their significance for peptide and protein characterization such as the advent and practical consequences of electrospray ionization (ESI) and matrix-assisted laser desorption/ionization (MALDI) are covered, including work done with triple quads, the development of time-of-flight (TOF) instruments and new ion traps and going on to the more recent work on the full characterization of the Proteome with ion traps, TOF instruments and new ionization and tagging techniques for protein sequencing.