Estimating the affinity of protein-ligand complex from changes to the charge-state distribution of a protein in electrospray ionization mass spectrometry

The detection of low affinity interactions between proteins and ligands by biophysical methods is challenging. It is often necessary to use competition methods that are time consuming and require well characterized known binders. A mass spectrometry approach is presented for identifying low affinity protein-ligand binding which does not require direct detection of the parent protein-ligand complex but depends on characteristic changes observed in the protein mass spectrum. We observe that on titration of ligand there are characteristic ‘charge-state shifts’ which manifest as changes in the relative intensities of protein peaks that correlate with the degree of protein-ligand complex formation. We suggest that use of this phenomenon will be particularly suitable for the identification of low affinity complexes where the intensity of any complex ion would be close to noise.     

Electrospray identification of new polyoxochromate species

Electrospray ionization mass spectrometry (ESI MS) has been conducted on the ammonium and alkali metal (A=Li⁺, Na⁺ and K⁺) dichromate systems. A large number of previously unknown polyoxochromate species have been characterized. Major series that have been identified include [A_x+1H_xCr^VI_xO_4x]⁺ (Li⁺, x=1-5; Na⁺, x=1-7; K⁺, x=1-4) and [A_2x−1Cr^VI_xO_4x−1]⁺ (Li⁺, x=2, 3; Na⁺, x=2-4; K⁺, x=2, 3) in the alkali metal dichromate systems, and [HCr^VI_xO_3x+1]⁻ (x=1-5) in the ammonium dichromate system. Several series also contain mixed oxidation state species, ranging from Cr(V) to Cr(II) in conjunction with Cr(VI), which is consistent with the ease of reduction of Cr(VI). Negative ion ESI MS spectra clearly demonstrate the existence of [HCrO₄]⁻ as the most abundant ion at −20 V, suggesting that its existence in solution is not just hypothetical, as was previously thought. The polymerization units for the series observed include {AHCrO₄}, {A₂CrO₄} and {CrO₃}, with the latter prominent in the alkali metal systems. This presumably arises from the fragmentation of dichromate, A₂Cr₂O₇→{A₂CrO₄}+{CrO₃}. Moreover, the ESI MS of the dichromate compounds have illustrated that the preservation of tetrahedral stereochemistry is of paramount importance for these systems, which leads to only limited polymerization compared to the related molybdate and tungstate systems.     

A method for profiling gangliosides in animal tissues using electrospray ionization-tandem mass spectrometry

Gangliosides are critical in many functions of mammalian cells but present as a minor lipid component with many molecular species of subtle differences. Conventional strategies for profiling gangliosides suffer from poor reproducibility, low sensitivity, and low-throughput capacity. Prior separation of gangliosides by thin-layer chromatography and/or high-performance liquid chromatography not only was laborious and tedious but also could introduce uneven losses of molecular species. We developed a new strategy of using electrospray ionization-tandem mass spectrometry (ESI-MS/MS) to profile gangliosides with high-throughput potential. This strategy involves three new findings: (i) collision-induced fragmentation of gangliosides gave rise to a common ion of m/z 290, a derivative of N-acetylneuraminic acid; (ii) phospholipids exert a profound suppression of ganglioside detection in ESI-MS/MS to prevent a direct detection in total cellular lipid extracts; and (iii) enrichment of gangliosides in the aqueous phase from total cellular lipid extracts eliminates the damping effect of phospholipids and permits direct precursor scan.     

Native mass spectrometry for understanding dynamic protein complex

Biomolecules have evolved to perform specific and sophisticated activities in a highly coordinated manner organizing into multi-component complexes consisting of proteins, nucleic acids, cofactors or ligands. Understanding such complexes represents a task in earnest for modern bioscience. Traditional structural techniques when extrapolating to macromolecules of ever increasing sizes are confronted with limitations posed by the difficulty in enrichment, solubility, stability as well as lack of homogeneity of these complexes. Alternative approaches are therefore prompted to bridge the gap, one of which is native mass spectrometry. Here we demonstrate the strength of native mass spectrometry, used alone or in combination with other biophysical methods such as analytical ultracentrifugation, small-angle neutron scattering, and small-angle X-ray scattering etc., in addressing dynamic aspects of protein complexes including structural reorganization, subunit exchange, as well as the assembly/disassembly processes in solution that are dictated by transient non-covalent interactions. We review recent studies from our laboratories and others applying native mass spectrometry to both soluble and membrane-embedded assemblies. This article is part of a Special Issue entitled “Biophysical Exploration of Dynamical Ordering of Biomolecular Systems” edited by Dr. Koichi Kato.     

Direct observation of covalent adducts with Cys34 of human serum albumin using mass spectrometry

The interactions of the unpaired thiol residue (Cys34) of human serum albumin (HSA) with low-molecular-weight thiols and an Au(I)-based antiarthritic drug have been examined using electrospray ionization mass spectrometry. Early measurements of the amount of HSA containing Cys34 as the free thiol suggested that up to 30% of circulating HSA bound cysteine as a mixed disulfide. It has also been suggested that reaction of HSA with cysteine, occurs only on handling and storage of plasma. In our experiments, there were three components of HSA in freshly collected plasma from normal volunteers, HSA, HSA+cysteine, and HSA+glucose in the ratio approximately 50:25:25. We addressed this controversy by using iodoacetamide to block the free thiol of HSA in fresh plasma, preventing its reaction with plasma cysteine. When iodoacetamide was injected into a vacutaner tube as blood was collected, the HSA was modified by iodoacetamide, with 20-30% present as the mixed disulfide with cysteine (HSA+cys). These data provide strong evidence that 20-30% of HSA in normal plasma contains one bound cysteine. Reaction of HSA with [Au(S(2)O(3))(2)](3-) resulted in formation of the adducts HSA+Au(S(2)O(3)) and HSA+Au. Reaction of HSA with iodoacetamide prior to treatment with [Au(S(2)O(3))(2)](3-) blocked the formation of gold adducts.     

Identification of neuropeptide FF-related peptides in human cerebrospinal fluid by mass spectrometry

Several neuropeptide FF (NPFF)-related peptides, known as modulators of the opioid system, have been previously characterized in bovine and rodent brain. Reverse-phase high pressure liquid chromatography (HPLC) fractions of a human with normal pressure hydrocephalus cerebrospinal fluid (CSF), co-migrating with NPFF-related synthetic peptides, were characterized by capillary HPLC coupled on-line to nanospray ion trap tandem mass spectrometry. Two peptides present in the pro-NPFF(A) precursor, NPAF (AGEGLNSQFWSLAAPQRF-NH2) and NPSF (SLAAPQRF-NH2), were identified. The monitoring of NPFF-related peptides in human CSF can be helpful to understand their roles in pain sensitivity.     

Determination of iodide in urine using electrospray ionization tandem mass spectrometry

A rapid and sensitive electrospray ionization (ESI) tandem mass spectrometry (MS–MS) procedure was developed for the determination of iodide (I⁻). A gold (Au) and I⁻ complex was formed immediately after the addition of the chelating agent NaAuCl₄ to I⁻ solution, and was extracted with methyl isobutyl ketone. One to five microliters of the extract were injected directly into an ESI–MS–MS instrument. I⁻ quantification was performed by selecting reaction monitoring of the product ion I⁻ at m/z 127 derived from the precursor ion ¹⁹⁷AuI₂⁻ at m/z 451. I⁻ concentration was measured in the quantification range from 10⁻⁷ to 10⁻⁵ M using 50 μL of solution within 10 min. Iodate was reduced to I⁻ with ascorbic acid and determined. I⁻ concentration in reference urine 2670a was measured after treatments.     

Electrospray ionization mass spectrometry in the study of biomolecular non-covalent interactions

In the past mass spectrometry has been limited to the study of small, stable molecules, however, with the emergence of electrospray ionization mass spectrometry (ESI-MS) large biomolecules as well as non-covalent biomolecular complexes can be studied. ESI-MS has been used to study non-covalent interactions involving proteins with metals, ligands, peptides, oligonucleotides, as well as other proteins. Although complementary to other well-established techniques such as circular dichroism and fluorescence spectroscopy, ESI-MS offers some advantages in speed, sensitivity, and directness particularly in the determination of the stoichiometry of the complex. One major advantage is the ability of ESI-MS to provide multiple signals each arising from a distinct population within the sample. In this review I will discuss some of the different types of non-covalent biomolecular interactions that have been studied using ESI-MS, highlighting examples which show the efficacy of using ESI-MS to probe the structure of biomolecular complexes.     

Mass spectrometric investigation of the DNA-binding properties of an anthracycline with two trisaccharide chains

Cosmomycin D (CosD) is an anthracycline that has two trisaccharide chains linked to its ring system. Gel electrophoresis showed that CosD formed stable complexes with plasmid DNA under conditions where daunorubicin (Dn) and doxorubicin (Dx) dissociated to some extent during the experiments. The footprint and stability of CosD complexed with 10- and 16 mer DNA was investigated using several applications of electrospray ionisation mass spectrometry (ESI-MS). ESI-MS binding profiles showed that fewer CosD molecules bound to the sequences than Dn or Dx. In agreement with this, ESI-MS analysis of nuclease digestion products of the complexes showed that CosD protected the DNA to a greater extent than Dn or Dx. In tandem MS experiments, all CosD–DNA complexes were more stable than Dn- and Dx-DNA complexes. These results support that CosD binds more tightly to DNA and exerts a larger footprint than Dn or Dx. ESI-MS investigations of the binding properties of CosD could be carried out rapidly and using only small amounts of sample.     

Ion-pairing reversed-phased chromatography/mass spectrometry of heparin

Heparin and heparin-derived components are widely applied anticoagulant drugs used for amongst other applications medical treatment of deep vein thrombosis and pulmonary embolism. Depolymerisation of native heparin results in complex mixtures of sulfated linear oligosaccharides that are usually not well characterised. In order to further characterise such mixtures, two on-line ion-pairing reverse-phased chromatography electrospray ionisation (ESI) mass spectrometry methods have been developed. One of the systems allows the determination of more than 200 components in a medium molecular weight heparin preparation, whereas the other system can be used to separate isomeric heparin oligosaccharides after previous separation according to size. This latter system allows semi-preparative isolation of isomeric heparin oligosaccharides. The experimental setup includes on-line cation exchange in order to prevent the ion-pairing reagent from entering the mass spectrometer.     

Oxidation of mannosyl oligosaccharides by hydroxyl radicals as assessed by electrospray mass spectrometry

The hydroxyl radicals are widely implicated in oxidation of carbohydrates during biological and industrial processes being responsible for their structural modifications and causing functional damage. The identification of intermediate oxidation products is hampered by a lack of reliable sensible methods for their detection. In this study, the oxidation of two models of galactomannans (Man₃ and GalMan₂) has been studied in reaction with hydroxyl radical generated by Fenton reaction. The oxidation patterns were assessed using preparative ligand-exchange/size-exclusion chromatography (LEX/SEC) coupled with tandem electrospray mass spectrometry (ESI-MS/MS). This allowed the identification of derived oligosaccharides (OS) containing hexuronic, hexonic, pentonic and erythronic acid residues and neutral OS bearing hydroperoxy, hydrated carbonyl moieties and residues from pyranosyl ring cleavage. The depolymerization products have been also detected upon oxidation of oligomers. This study allowed developing a simple, effective ‘fingerprinting’ protocol for detecting the damage done to mannans by oxidative radicals.     

On the identification of ionic species of neutral halogen dimers, monomers and pincer type palladacycles in solution by electrospray mass and tandem mass spectrometry

Electrospray (ESI) mass spectra analysis of acetonitrile solutions of a series of neutral chloro dimers, pincer type, and monomeric palladacycles has enabled the detection of several of their derived ionic species. The monometallic cationic complexes Pd[κ¹-C,κ¹-N,κ¹-S-C(CH₃S-2-C₆H₄)C(Cl)CH₂N(CH₃)₂]⁺ (1a) and [Pd[κ¹-C,κ¹-N,κ¹-S-C(CH₃S-2-C₆H₄)C(Cl)CH₂N(CH₃)₂](CH₃CN)]⁺ (1b) and the bimetallic cationic complex [κ¹-C,κ¹-N,κ¹-S-C(CH₃S-2-C₆H₄)C(Cl)CH₂N(CH₃)₂]Pd-Cl-Pd[κ¹-C,κ¹-N,κ¹-S-C(CH₃S-2-C₆H₄)C(Cl)CH₂N(CH₃)₂]⁺ (1c) were detected from an acetonitrile solution of the pincer palladacycles Pd[κ¹-C,κ¹-N,κ¹-S-C(CH₃S-2-C₆H₄)C(Cl)CH₂N(CH₃)₂](Cl) 1. For the dimeric compounds {Pd[κ¹-C,κ¹-N-C(Y-2-C₆H₄)C(Cl)CH₂N(CH₃)₂](μ-Cl)}₂ (2, Y=H and 3, CF₃), highly electronically unsaturated palladacycles [Pd[κ¹-C,κ¹-N-C(Y-2-C₆H₄)C(Cl)CH₂N(CH₃)₂]⁺ (2d, 3d) and their mono and di-acetonitrile adducts, namely, [Pd[κ¹-C,κ¹-N-C(Y-2-C₆H₄)C(Cl)CH₂N(CH₃)₂](CH₃CN)]⁺ (2e, 3e) and [Pd[κ¹-C,κ¹-N-C(Y-2-C₆H₄)C(Cl)CH₂N(CH₃)₂](CH₃CN)₂]⁺ (2f and 3f) were detected together with the bimetallic complex [Pd[κ¹-C,κ¹-N-C(Y-2-C₆H₄)C(Cl)CH₂N(CH₃)₂]-Cl-Pd[κ¹-C,κ¹-N-C(Y-2-C₆H₄)C(Cl)CH₂N](CH₃)₂]⁺ (2a, 3a) and its acetonitrile adducts [κ¹-C,κ¹-N-C(Y-2-C₆H₄)C(Cl)CH₂N(CH₃)₂](CH₃CN)Pd-Cl-Pd[ κ¹-C,κ¹-N-C(Y-2-C₆H₄)C(Cl)CH₂N(CH₃)₂]⁺ (2b, 3b) and [κ¹-C,κ¹-N-C(Y-2-C₆H₄)C(Cl)CH₂N(CH₃)₂](CH₃CN)Pd-Cl-Pd[κ¹-C, κ¹-N-C(Y-2-C₆H₄)C(Cl)CH₂N(CH₃)₂(CH₃CN)]⁺ (2c, 3c). The dimeric palladacycle {Pd[κ¹-C,κ¹-N-C(CH₃O-2-C₆H₄)C(Cl)CH₂N(CH₃)₂](μ-Cl)}₂ (4) is unique as it behaves as a pincer type compound with the OCH₃ substituent acting as an intramolecular coordinating group which prevents acetonitrile full coordination, thus forming the cationic complexes [(C₆H₄(o-CH₃O)CC(Cl)CH₂N(CH₃)₂-κO,κC,κN)Pd]⁺ (4b), [(C₆H₄(o-CH₃O)CC(Cl)CH₂N(CH₃)₂- κO,κC,κN)Pd(CH₃CN)]⁺ (4c) and [(C₆H₄ (o-MeO)CC(Cl)CH₂N(CH₃)₂-κO, κC,κN)Pd-Cl-Pd(C₆H₄(o-CH₃O)CC(Cl)CH₂N(CH₃)₂-κO,κC,κN)]⁺ (4a). ESI-MS spectra analysis of acetonitrile solutions of the monomeric palladacycles Pd[κ¹-C,κ¹-N-C(Y-2-C₆H₄)C(Cl)CH₂N(CH₃)₂](Cl)(Py) (5, Y=H and 6, Y=CF₃) allows the detection of some of the same species observed in the spectra of the dimeric palladacycles, i.e., monometallic cationic 2d-3d, 2e-3e and {Pd[κ¹-C,κ¹-N-C(Y-2-C₆H₄)C(Cl)CH₂N(CH₃)₂](Py)}⁺ (5a, 6a) and {Pd[κ¹-C,κ¹-N-C(Y-2-C₆H₄)C(Cl)CH₂N(CH₃)₂](CH₃CN)(Py)}⁺ (5b, 6b) and the bimetallic 2a, 3a, 2b, 3b, 2c and 3c. In all cationic complexes detected by ESI-MS, the cyclometallated moiety was intact indicating the high stability of the four or six electron anionic chelate ligands. The anionic (chloride) or neutral (pyridine) ligands are, however, easily replaced by the acetonitrile solvent.     

Quadrupole ion-trap mass spectrometry to locate fatty acids on lipid A from Gram-negative bacteria

The structure of lipid A released by mild acid hydrolysis from lipopolysaccharide from two strains of Shigella flexneri with different degrees of acylation was characterized using electrospray ionization (ESI) and ion-trap mass spectrometry. The lipid A was analyzed underivatized with ESI in negative-ion mode. With multiple stages of fragmentation (MS(n)), both the degree of acylation and the positions of the fatty acids on the disaccharide backbone could be determined. It was possible to determine the degree of acylation by the MS(n) technique, where in each MS stage the parent ion was an ion where one fatty acid had been eliminated. One way to determine the location of the fatty acids was by identifying cross-ring fragments of the reducing sugar from parent ions containing different numbers of fatty acids. Another was by identifying a possible charge-driven release of fatty acids situated close to a phosphate group. The fatty acids were otherwise eliminated by a charge-remote fragmentation mechanism. The combined data show the usefulness of ion-trap mass spectrometers for this type of analysis.     

Application of mass spectrometry to determine the activity and specificity of pectin lyase A

Electrospray ionization (ESI) with quadrupole ion-trap mass spectrometry was used to assess the activity and specificity of the enzyme pectin lyase A (PLA) (EC 4.2.2.10) on model pectins with varying degrees and patterns of methyl esterification. PLA is a pectinase which cleaves alpha-(1-->4)-glycosidic linkages in pectin by a trans-elimination process. Using pectins with different degrees and patterns of methyl esterification, there was a significant variation in the activity rate of PLA. The enzymatic products generated at various time intervals were structurally analyzed by mass spectrometry to determine the specificity of PLA. Although the preferred substrate for PLA is fully methyl esterified polygalacturonate, cleavage was also observed with a non-methyl esterified galacturonic acid residue on either the non-reducing end or the reducing end. The current study shows that although PLA prefers fully methyl esterified substrates it can also accept partially esterified ones. It also demonstrates the suitability of ESI ion-trap mass spectrometry in determining enzyme specificities.     

Characterisation of intact microorganisms using electrospray ionisation mass spectrometry

We report the first application of electrospray ionisation mass spectrometry (ESI-MS) for the reproducible characterisation of strains of intact Gram-negative and Gram-positive bacteria. Electrospray ionisation was performed in both the positive and negative ion modes and the spectra obtained from Escherichia coli and Bacillus cereus were very information rich. Several of the observed negative mass ion fragments from E. coli could be assigned to specific fragmentation from bacterial phospholipids.Cluster analyses of these spectra showed that ESI-MS could be used to discriminate between these microorganisms to below species level. Therefore we conclude that ESI-MS constitutes a powerful approach to the characterisation and speciation of intact microorganisms.     

Comparison of folate quantification in foods by high-performance liquid chromatography-fluorescence detection to that by stable isotope dilution assays using high-performance liquid chromatography-tandem mass spectrometry

A comparison study on folate quantitation was carried out between the recently developed stable isotope dilution assay using liquid chromatography-tandem mass spectrometry (LC-MS-MS) and the frequently used HPLC with fluorimetric detection (LC-FD). By applying LC-MS-MS, spinach, wheat bread, beef, and blood plasma were found to contain 159.2, 19.8, 1.2, and 5.6 microg/100 g total folates, respectively, whereas the respective quantitative data obtained by LC-FD were 95.5, 16.2, 0.7, and 6.8 microg/100 g. In all samples, LC-MS-MS revealed superior selectivity and precision and circumvented the shortcomings of conventional LC techniques, i.e., ambiguous peak assignment as well as high detection limits for 5-formyltetrahydrofolate, 10-formylfolic acid, and folic acid. The affinity chromatography columns used in this study showed excellent cleanup performance and permitted detection limits as low as 0.1, 0.5, 0.1, 0.08, and 0.1 microg/100 g for tetrahydrofolate (H(4)folate), 5-methyl-H(4)folate, 5-formyl-H(4)folate, 10-formylfolate, and pteroylglutamic acid, respectively. Thus, a 10-fold higher sensitivity compared to solid-phase anion-exchange cartridges was achieved. However, affinity chromatography columns revealed a significantly higher affinity toward the natural vitamers than to the racemic isotopomeric standards, which has to be considered when applying the latter in stable isotope dilution assays.     

Kinetics of an enzyme-catalyzed reaction measured by electrospray ionization mass spectrometry using a simple rapid mixing attachment

Mass spectrometry offers a potential means of measuring virtually all enzyme-catalyzed reactions by simultaneously measuring the concentrations of substrates, products, and intermediates where there are differences in mass between them. To perform these measurements the reaction mixture must be aged for different times and then ionized. Electrospray ionization mass spectrometry provides the most direct means of measuring these reactions. Here we describe a simple reaction mixing and ageing attachment for an electrospray ionization mass spectrometer, built from commercially available components. We have employed this device to measure the kinetics of a model reaction, namely the hydrolysis of N2-(carbobenzyloxy)-L-lysine-p-nitrophenyl ester-catalyzed by trypsin. In this way we were able to measure the kinetics of substrate depletion, product formation, and changes in both free enzyme and acyl-enzyme intermediate concentration in the approach to steady state. With this device we were able to measure reaction times down to about 640 ms.     

Fragmentation pattern of underivatised xylo-oligosaccharides and their alditol derivatives by electrospray tandem mass spectrometry

Maltopentaose and olive pulp xylo-oligosaccharides and the correspondent alditol derivatives were analysed by ESI-MS and ESI-MS/MS. The ESI-MS spectrum of maltopentaose and maltopentaose alditols showed [M+Na]⁺and [M+H]⁺ ions. ESI-MS spectrum of xylo-oligosaccharides and their alditols showed [M+Na]⁺of neutral (Xyl_3–6) and acidic (Xyl_2–3MeGlcA and Xyl_2–3GlcA) xylo-oligosaccharides. The ESI-MS/MS spectra of maltopentaose and underivatised xylo-oligosaccharides presented fragments of glycosidic cleavages attributed to B/Z and C/Y ions. On the other hand, MS/MS spectra of the correspondent alditols showed glycosidic cleavages unambiguously identified as B-type and Y-type ions. Y-type fragment ions showed higher abundance in the MS/MS spectra of the alditol derivatives when compared to the non-reduced samples. The study of the oligoxylosyl alditols fragmentation permits to distinguish fragmentation pathways that occur both from the reducing end and from the non-reducing end of the xylan chain, allowing to obtain more information about the localization of the acidic substituent along the glucuronoxylan backbone.     

Automated affinity chromatography measurements of compound mixtures using a lab-on-valve apparatus coupled to electrospray ionization mass spectrometry

We report a fully automated affinity chromatography system using a lab-on-valve (LOV) apparatus coupled to an electrospray ionization ion-trap mass spectrometer (ESI-MS). The system allows simultaneous measurements of multiple ligand affinities to proteins immobilized on beads. Bead regeneration, column repacking, and repetitive measurements are achieved on the time scale of several minutes. In this study, the system was used to screen the binding of a peptide mixture to human and Trypanosoma brucei (T. brucei) truncated Pex5 (tPex5) proteins. Equilibrium dissociation constants (K(d)) were measured for T. brucei tPex5 and compared to the values obtained by a fluorescence-based competition assay. The three peptides that showed affinity toward tPex5 had K(d) values that were comparable in magnitude (within a factor of 5) and showed the same ranking order as those from manual fluorescence measurements. With 12 min of sample infusion, the entire sample-to-sample cycle takes about 15 min and can be repeated without any preparation between runs. For T. brucei tPex5 affinity measurements, 1 mg of protein was sufficient for 35 repetitive analyses in the automated LOV-ESI-MS apparatus. The system allows rapid determination of K(d) in the range of 10(-5)-10(-7) M for sample mixtures and is suitable for screening a large number of compounds against multiple proteins.