Fragmentation of intra-peptide and inter-peptide disulfide bonds of proteolytic peptides by nanoESI collision-induced dissociation

Characterisation and identification of disulfide bridges is an important aspect of structural elucidation of proteins. Covalent cysteine-cysteine contacts within the protein give rise to stabilisation of the native tertiary structure of the molecules. Bottom-up identification and sequencing of proteins by mass spectrometry most frequently involves reductive cleavage and alkylation of disulfide links followed by enzymatic digestion. However, when using this approach, information on cysteine-cysteine contacts within the protein is lost. Mass spectrometric characterisation of peptides containing intra-chain disulfides is a challenging analytical task, because peptide bonds within the disulfide loop are believed to be resistant to fragmentation. In this contribution we show recent results on the fragmentation of intra and inter-peptide disulfide bonds of proteolytic peptides by nano electrospray ionisation collision-induced dissociation (nanoESI CID). Disulfide bridge-containing peptides obtained from proteolytic digests were submitted to low-energy nanoESI CID using a quadrupole time-of-flight (Q-TOF) instrument as a mass analyser. Fragmentation of the gaseous peptide ions gave rise to a set of b and y-type fragment ions which enabled derivation of the sequence of the amino acids located outside the disulfide loop. Surprisingly, careful examination of the fragment-ion spectra of peptide ions comprising an intramolecular disulfide bridge revealed the presence of low-abundance fragment ions formed by the cleavage of peptide bonds within the disulfide loop. These fragmentations are preceded by proton-induced asymmetric cleavage of the disulfide bridge giving rise to a modified cysteine containing a disulfohydryl substituent and a dehydroalanine residue on the C-S cleavage site.     

Structural elucidation of O-linked glycopeptides by high energy collision-induced dissociation

O-linked glycopeptides that bear a GalNAc core with and without the presence of sialic acid have been analyzed by high energy collision-induced dissociation (CID). We show that the CID spectra from the glycosylated precursor ions contain sufficient information to identify the peptide sequence and to determine the glycosylated site(s). Asialo O-linked glycopeptides, previously prepared from a tryptic digest of bovine fetuin were studied. One of the glycopeptides contained only a single Hex (hexose)-HexNAc (N-acetylhexosamine) substitution at Thr²⁶², whereas the other exhibited Hex-HexNAc moieties at both Thr²⁶² and Ser²⁶⁴. In addition, sialo and asialo fetuin glycopeptides from a pronase digest were derivatized with t-butoxycarbonyl-tyrosine, and characterized by high energy CID analysis. The presence of a Galβ(1,3)GalNAc core structure at Ser²⁶⁴ was confirmed by using the substrate specificity of endo-α-N-acetylgalactosaminidase. These studies revealed the presence of a β-galactosidase specific for β(1,4) linkages in the endo-α-N-acetylgalactosaminidase preparation employed. Finally, the relative stability of N-and O-glycosyl bonds to high energy CID is addressed based upon comparison of the behavior of a synthetic N-linked glycopeptide with analogous O-linked structures.     

Structure elucidation of cyclic pyoverdins and examination of rearrangement reactions in MS/MS experiments by determination of exact product ion masses

Structure elucidation of naturally occurring linear and cyclic peptidic compounds can be complicated by rearrangement reactions induced upon collision activation (CA) when parts of the molecule migrate, suggesting incorrect substitution patterns. Such complex rearrangements are examined and discussed for two iron complexing compounds produced by the bacterial genus Pseudomonas (so-called pyoverdins). Various MS2- and MS3-product ion experiments were performed using a quadrupole-ion trap (QIT) at low resolution and a FT-ICR at high resolution allowing accurate mass determinations. The results of the multidimensional study confirm the proposed processes. On the basis of the series of tandem-MS experiments the structure of a new pyoverdin from a P. fluorescens strain [PVD(D47)] is deduced.     

Synthetic glycopeptides and glycoproteins as tools for biology

Investigations into the roles of protein glycosylation have revealed functions such as modulating protein structure and localization, cell-cell recognition, and signaling in multicellular systems. However, detailed studies of these events are hampered by the heterogeneous nature of biosynthetic glycoproteins that typically exist in numerous glycoforms. Research into protein glycosylation, therefore, has benefited from homogeneous, structurally-defined glycoproteins obtained by chemical synthesis. This tutorial review focuses on recent applications of homogeneous synthetic glycopeptides and glycoproteins for studies of structure and function. In addition, the future of synthetic glycopeptides and glycoproteins as therapeutics is discussed.     

Analysis of glycoproteins, glycopeptides and glycoprotein-derived oligosaccharides by high-performance capillary electrophoresis

Recent developments in the analysis of glycoproteins by high-performance capillary electrophoresis are reviewed, with emphasis on their carbohydrate chains. Glycoforms of glycoproteins were directly separated from each other by careful optimization of the analytical conditions. Glycopeptides in tryptic digests were separated and the peptides carrying glycosylation sites were differentiated from others. Released oligosaccharide chains were separated at a low wavelength. Precolumn derivatization by various methods extended the utility of both the absorption at a low wavelength. Precolumn derivatization by various methods extended the utility of both the separation mode and detection technique. Dual mode analysis after derivatization permitted reliable identification and quantification without references.     

Structure elucidation and HPLC-MS/MS determination of a potential biomarker for estradiol administration in cattle

Administration of hormonal compounds as growth promoters in livestock farming was banned by Council Directive 96/22/EC. However, this kind of substances is sometimes reported within the framework of European monitoring residue plans. Various analytical methods have been previously developed to screen for their misuse, and they are now especially efficient for monitoring the illegal administration of synthetic and semisynthetic hormones. Nevertheless, proving an exogenous administration of hormones from natural origin (i.e., estradiol-17β or progesterone) still remains a challenge for European authorities. These target compounds are indeed always present in the animal matrix, and the establishment of reference thresholds appears very difficult because of the extreme variability existing among animals. In 2011, a metabolomics study was performed on serum samples obtained from cows treated with estradiol-17β (or its ester estradiol benzoate) and from control animals using a high-performance liquid chromatography (HPLC)-LTQ-Orbitrap system. After appropriate data processing and multivariate statistical analysis (orthogonal partial least squares discriminant analysis), it was possible to highlight one potential biomarker candidate of estradiol treatments in bovine animals. Now, this biomarker has been structurally elucidated as a dipeptide, and its usefulness has been tested through a targeted HPLC-MS/MS method. Its presence in the previous samples has been confirmed and also in additional samples from estradiol-treated animals.     

Antigiardial activity of glycoproteins and glycopeptides from Ziziphus honey

Natural honey contains an array of glycoproteins, proteoglycans and glycopeptides. Size-exclusion chromatography fractionated Ziziphus honey proteins into five peaks with molecular masses in the range from 10 to >200 kDa. The fractionated proteins exhibited in vitro activities against Giardia lamblia with IC₅₀ values ≤ 25 μg/mL. Results indicated that honey proteins were more active as antiprotozoal agents than metronidazole. This study indicated the potential of honey proteins and peptides as novel antigiardial agents.     

The resistance of metallothionein to proteolytic digestion: an LC-MS/MS analysis

Metallothioneins (MTs) are a family of cysteine-rich metalloproteins which strongly bind to heavy metals, such as Cd(II), Zn(II), and Cu(I). Previous works by other group using gel electrophoresis and fluorescence showed MTs were resistant to proteolytic digestion by a variety of enzymes, raising the difficulties in proteomic identification of MTs. The present work was attempted to analyze the resistance of MTs to trypsin using LC with MS/MS (LC-MS/MS), which was able to determine the sequences of the produced peptides and thus precisely characterize the cleavages. The results showed that metal-saturated MTs were completely resistant to trypsin. This resistance problem could be overcome by the addition of EDTA to MT samples, which rendered MTs readily digested into peptides and identified by MS/MS. Interestingly, the partially metal binding MTs were digested into peptides predominantly with miss cleavages which were well dependent on the amount of heavy metals bound to MTs. An explanation for these observations was proposed. The potential applications of the MT's resistance to trypsin in isolation and identification of MTs in complex mixtures such as cultured cells was demonstrated. The preliminary data also showed the same proteomic approach of proteolytic digestion followed by MS/MS analysis may provide information on metal binding status of MTs, along with the identification of MTs in a mixture.     

Structure elucidation and conformational analysis of a fused cyclopentanopyrazolidinol

From the reaction of 2‐acetylcyclopentanone with benzoylhydrazine, the cyclopentanopyrazole derivative 4 was obtained as the only product. The structural assignment of this compound and also of the hydroxypyrazoline 3 , used as a model compound, was established by analysis of their NMR spectra (¹H, ¹³C, COSY, NOESY, HETCOR and COLOC). Copyright © 2002 John Wiley & Sons, Ltd.     

Stereochemical analysis of deuterated alkyl chains by MS/MS

Vicinally deuterated sec-alkyl phenyl ethers, CH(3)(CH(2))(m)()CH(OPh)CHD(CH(2))(n)()CH(3), display significant differences in mass spectra between threo and erythro stereoisomers. MS/MS experiments, in which parent ions of a single mass are selected and their fragmentation patterns subsequently measured, show that alkene expulsion represents virtually the only decomposition pathway. Two types of MS/MS experiment are reported: mass-analyzed ion kinetic energy (MIKE) spectroscopy of metastable ions and collisionally activated decomposition (CAD) of stable ions. The expulsion of a deuterated alkene from a monodeuterated precursor yields ionized phenol, PhOH(*)()(+) (m/z 94). The expulsion of an undeuterated alkene yields PhOD(*)()(+) (m/z 95). Without exception, the ratios (PhOD(*)()(+)/PhOH(*)()(+)) from precursors in the threo series have values greater than their diastereomers in the erythro series. The ratio of ratios, r = PhOD(*)()(+)/PhOH(*)()(+) for the threo divided by PhOD(*)()(+)/PhOH(*)()(+) for the erythro, has a value of 1.2 for the 2-phenoxy-3-deuteriobutanes and larger values for all of the higher homologues up through the monodeuterated phenoxyoctanes (m + n = 4). The highest degree of stereoselectivity, r = 5.8, is measured for 3-phenoxy-4-deuteriohexane. Experiments with multiply deuterated analogues show that alkene elimination is highly regioselective, unlike the corresponding decompositions of ionized sec-alcohols or their acetates. The fact that a large fraction of ionized sec-alkyl phenyl ethers undergo stereospecific syn-elimination means that mass spectrometry has a useful capacity to distinguish one isotopically labeled diastereomer from another.     

Off-line hyphenation of boronate affinity monolith-based extraction with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry for efficient analysis of glycoproteins/glycopeptides

Boronate affinity materials have attracted increasing attentions as sample enrichment platforms for glycoproteomic analysis in recent years. However, most of the boronate affinity materials that have already employed for proteomic analysis are suffering from apparent disadvantages, such as alkaline pH for binding, weak affinity, and relatively poor selectivity. Benzoboroxoles are a unique class of boronic acids which have showed excellent binding properties for the recognition of cis-diol-containing compounds. Recently, a 3-carboxy-benzoboroxole-functionalized monolithic column had been reported and it had exhibited the best selectivity and affinity as well as the lowest binding pH among all reported boronate affinity monolithic columns. In this study, an off-line hyphenation of this boronate affinity monolithic column-based extraction with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) was developed and the powerfulness of this hyphenated approach in the analysis of glycoproteins and glycopeptides in complex samples was investigated. The approach was first applied to the analysis of glycopeptides in the tryptic digest of horseradish peroxidase (HRP). Totally 22 glycopeptides were identified. To the best of our knowledge, this is the best performance among all the boronic acid-functionalized materials. We further employed this approach to the analysis of intact proteins in human saliva. Totally 6 intact glycoproteins were successfully identified. As comparison, when the samples were analyzed without extraction, only a few glycopeptides were identified from the tryptic digest of HRP while no glycoproteins were found from the saliva samples.     

Structure elucidation of (+)-amphidinolide a by total synthesis and NMR chemical shift analysis

The structure elucidation of (+)-amphidinolide A, a cytotoxic macrolide, has been accomplished by employing a combination of NMR chemical shift analysis and total synthesis. Using the reported structure as a starting point, a number of diastereomers of amphidinolide A were prepared. The deviations of the chemical shifts of key protons in each isomer relative to the values reported for the isolated material were used to determine the locations of the errors in relative stereochemistry. The spectroscopic data for our proposed structure of (+)-amphidinolide A and the isolated material are in excellent agreement. The key step, a [Cp*Ru(MeCN)3]PF6-catalyzed alkene-alkyne coupling, was used to form the 20-membered ring in the final step of the synthesis.     

Recent advances in the MS analysis of glycoproteins: Theoretical considerations

Protein glycosylation is involved in a broad range of biological processes that regulate protein function and control cell fate. As aberrant glycosylation has been found to be implicated in numerous diseases, the study and large-scale characterization of protein glycosylation is of great interest not only to the biological and biomedical research community, but also to the pharmaceutical and biotechnology industry. Due to the complex chemical structure and differing chemical properties of the protein/peptide and glycan moieties, the analysis and structural characterization of glycoproteins has been proven to be a difficult task. Large-scale endeavors have been further limited by the dynamic outcome of the glycosylation process itself, and, occasionally, by the low abundance of glycoproteins in biological samples. Recent advances in MS instrumentation and progress in miniaturized technologies for sample handling, enrichment and separation, have resulted in robust and compelling analysis strategies that effectively address the challenges of the glycoproteome. This review summarizes the key steps that are involved in the development of efficient glycoproteomic analysis methods, and the latest innovations that led to successful strategies for the characterization of glycoproteins and their corresponding glycans. As a follow-up to this work, we review innovative capillary and microfluidic-MS workflows for the identification, sequencing and characterization of glycoconjugates.     

Applications of CE-ESI-MS/MS analysis to structural elucidation of methylenecyclohexane ozonolysis products in the particle phase

The composition of secondary organic aerosol (SOA) from the gas phase ozonolysis of methylenecyclohexane was analyzed in a series of indoor aerosol chamber experiments. Capillary electrophoresis-electrospray ionization-ion trap mass spectrometry (CE/ESI-ITMS) was used for qualitative and quantitative analysis of SOA constituents. A number of dicarboxylic acids in the range of C(5)-C(6), such as adipic acid and glutaric acid, were found as major components of the organic products. Besides these smaller compounds, the formation of higher-molecular-weight compounds were observed under both neutral and acidic conditions. MS/MS experiments were carried out in order to obtain information on the monomer units and the structure of the dimers. MS(2) experiments of the two most prominent dimers with a mass-to-charge ratio (m/z) of 257 and m/z 273 yielded common fragments of m/z 83, 129 or 145. Based on the fragmentation patterns, these dimers are tentatively identified as carboxylate ester acids containing a unit of adipic acid in the structure. The dimer with m/z 257 was nearly 60% of the total detected compounds for both the neutral and acidic seed particle experiments.     

Identification and structural elucidation of steroidal saponins from the root of Paris polyphylla by HPLC-ESI-QTOF-MS/MS

The root of Paris polyphylla (RPP) is widely used as a traditional Chinese medicine for a long time due to the good properties of heat-clearing and detoxicating, detumescence, sedation, acesodyne and haemostasis. To clarify on the bioactive substances and ensure the safety in clinical medication, a feasible and accurate strategy was developed by applying the high-performance liquid chromatography coupled to electrospray ionisation and quadrupole time-of-flight-mass spectrometry (HPLC-ESI-QTOF-MS/MS). Separation was performed an Agilent poroshell 120 EC-C18 column (2.7 × 100 mm, i.d., 2.7 μm) with 0.1% formic acid aqueous solution and acetonitrile as the mobile phase under gradient conditions. Based on the proposed strategy, 30 constituents, mainly including steroidal saponins, were characterised or tentatively identified, 2 of which were the first to be reported as the potential new steroidal saponins in RPP. In conclusion, the HPLC-ESI-QTOF-MS/MS is a feasible and credible technique to separate and identify steroidal saponins from botanical extracts.     

Pesticide residue analysis of fruit juices by LC-MS/MS direct injection. One year pilot survey

For this work, thirteen types of fruit juices (orange, pineapple, peach, apple, multifruit, mango, strawberry, tomato, pear, mandarin, grape, banana and grapefruit) were selected to develop an analytical method for the analysis of 53 pesticides by direct injection in LC-MS/MS. The preparation of the samples was very simple: an aliquot of the juice was centrifuged and it was ten-times diluted prior to analysis, which allowed reducing considerably the time and cost of the analyses. Besides, dilution of the samples permits reducing the amount of matrix going into the system, and thus, decreasing the matrix effects, so common in this type of commodities, opening the possibility to perform quantification with solvent based standards. Validation of the method was carried out in accordance with EU guidelines. Calibration curves covering three orders of magnitude were performed, and they were linear over the concentration range studied for all the matrices (from 0.1 to 100 μg L⁻¹). Practical limits of quantification were in the low μg L⁻¹ range, far below the maximum residue levels (MRLs) of the EU regulations, which do not set specific MRLs for juices, and in this cases of processed food, MRLs of the raw product are applied. Repeatability of the instrumental method was studied in all matrices, obtaining good intra- and inter-day relative standard deviations (RSDs). The proposed method was applied to 106 real fruit juice samples purchased in different local markets during a one-year survey in order to validate the suitability for routine analysis. 43% of the analysed samples gave positive results (higher than the practical limits of quantification).     

An optimized protocol for nano-LC-MALDI-TOF-MS coupling for the analysis of proteolytic digests of glycoproteins

Matrix-assissted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF-MS) analyses of complete proteolytic digests are often hampered by contaminations and the complexity of the sample. This results in suppression effects and the formation of adducts which are difficult to assign, thus leading to low scores in database searches. In particular, signals of post-translationally modified peptides such as glycopeptides are often of low intensity or completely suppressed. Online liquid chromatography electrospray ionization mass spectrometry (ESI-MS) can, in part, overcome this problem, but the analytes are completely consumed during the run. Coupling of nano-flow HPLC (nano-LC), microfractionation and MALDI-TOF-MS combines separation and high-sensitivity UV detection with the possibility of collecting fractionated peptides and preserving the sample for detailed mass spectrometric analyses. Here we report on an optimized protocol for nano-LC-MALDI-TOF-MS analyses of glycoproteins. This protocol improves spectral quality, resulting in better protein identification scores in database searches. Furthermore, post-translationally modified peptides could be detected with higher sensitivity by changing the experimental conditions, allowing assignment, localization and characterization of the respective carbohydrate substituents.     

Recent advances in the MS analysis of glycoproteins: Capillary and microfluidic workflows

Recent developments in bioanalytical instrumentation, MS detection, and computational data analysis approaches have provided researchers with capabilities for interrogating the complex cellular glycoproteome, to help gain a better insight into the cellular and physiological processes that are associated with a disease and to facilitate the efforts centered on identifying disease-specific biomarkers. This review describes the progress achieved in the characterization of protein glycosylation by using advanced capillary and microfluidic MS technologies. The major steps involved in large-scale glycoproteomic analysis approaches are discussed, with special emphasis given to workflows that have evolved around complex MS detection functions. In addition, quantitative analysis strategies are assessed, and the bioinformatics aspects of glycoproteomic data processing are summarized. The developments in commercial and custom fabricated microfluidic front-end platforms to ESI- and MALDI-MS instrumentation, for addressing major challenges in carbohydrate analysis such as sensitivity, throughput, and ability to perform structural characterization, are further evaluated and illustrated with relevant examples.