Performance of the computer algorithm COMPLX for the detection of protein complexes in the mass spectra of simulated biological mixtures

The performance of the algorithm COMPLX for detecting protein-ligand or other macromolecular complexes has been tested for highly complex data sets. These data contain m/z values for ions of proteins of the SWISS-PROT database within simulated biological mixtures where each component shares a similar molecular weight and/or isoelectric point (pI). As many as 1600 ion signals were entered to challenge the algorithm to identify ion signals associated with a single protein complex that has been ionised and detected within a mass spectrometer. Despite the complexity of such data sets, the algorithm is shown to be able to identify the presence of individual bimolecular complexes. The output data can be re-evaluated by the user as necessary in light of any additional information that is known concerning the nature of predicted associations, as well as the quality of the data-set in terms of errors in m/z values as a direct consequence of the mass calibration or resolution achieved. The data presented illustrates that the best results are obtained when output results are ranked according to the largest continuous series of ion pairs detected for a protein or macromolecule and its complex for which the ligand mass is assigned the lowest mass error.     

Band composition analysis: a new procedure for deconvolution of the mass spectra of organometallic compounds

A new chemometric procedure called band composition analysis (BCA) designed for the deconvolution of mass spectra of organometallics is proposed. BCA generates theoretical bands T(i), then combines them to obtain a model band M, which is finally compared with the experimental band E. All of these steps are realized with computer assistance. This modeling yields four parameters characterizing the experimental band: theoretical and model variances s(2) (theor) and s(2) (model), a fit factor alpha and a contribution x(i) from the theoretical band. If s(2) (theor) > 20 the band is deemed complex and needs modeling. The values alpha > 90 indicate that there is good agreement between the experimental and model bands. BCA is particularly effective for the modeling of complex isotopic bands often present in organometallics. Two illustrations of BCA for tetrabutyltin, C(16)H(36)Sn, and 1,1',2,2',3,3'-hexachloroferrocene, C(10)H(4)Cl(6)Fe, are shown.     

Automated deconvolution and deisotoping of electrospray mass spectra

Electrospray ionization (ESI) of peptides and proteins produces a series of multiply charged ions with a mass/charge (m/z) ratio between 500 and 2000. The resulting mass spectra are crowded by these multiple charge values for each molecular mass and an isotopic cluster for each nominal m/z value. Here, we report a new algorithm simultaneously to deconvolute and deisotope ESI mass spectra from complex peptide samples based on their mass-dependent isotopic mean pattern. All signals corresponding to one peptide in the sample were reduced to one singly charged monoisotopic peak, thereby significantly reducing the number of signals, increasing the signal intensity and improving the signal-to-noise ratio. The mass list produced could be used directly for database searching. The developed algorithm also simplified interpretation of fragment ion spectra of multiply charged parent ions.     

Binding constant determination of high-affinity protein-ligand complexes by electrospray ionization mass spectrometry and ligand competition

We describe an approach for the determination of binding constants for protein-ligand complexes with electrospray ionization mass spectrometry, based on the observation of unbound ligands competing for binding to a protein target. For the first time, dissociation constants lower than picomolar could be determined with good accuracy by electrospray ionization mass spectrometry. The presented methodology relies only on the determination of signal intensity ratios for free ligands in the low mass region. Therefore, all the advantages of measuring low masses with mass spectrometry, such as high resolution are preserved. By using a reference ligand with known binding affinity, the affinity of a second ligand can be determined. Since no noncovalently bound species are observed, assumptions about response factors are not necessary. The method is validated with ligands binding to avidin and applied to ligands binding to p38 mitogen-activated protein kinase.     

有机镓配合物的合成及其质谱

本文通过三环戊基镓与取代苯酚, 有机酸, 氨基酸反应合成了八个新的有机镓配合物, 这些配合物经过元素分析、质谱、核磁共振或红外光谱鉴定; 质谱研究表明这些配合物均以二聚体的形式存在。     

Electrospray mass spectrometry analysis of ferocenylketimines and their platinum(II) complexes

Ferrocenylketimines from ethylenediamine, trimethylenediamine, N-(2-hydroxyethyl)ethylenediamine and ferrocenecarboxaldehyde were prepared and characterized by elementary analysis, Fourier Transform infrared (FTIR), nuclear magnetic resonance (NMR) and electrospray mass spectrometry (ESMS). Corresponding platinum(II) complexes were also prepared and characterized by elementary analysis, FTIR and ESMS. The results of ESMS are discussed in terms of stability and show that the complexes are unstable and undergo cyclometallation under relatively mild conditions of ionization. This study has also evidenced the possibility of formation of complexes having two metal ions bound to one ligand instead of the more favorable chelates.     

Effect of stereochemistry on the electrospray ionization tandem mass spectra of transition metal chloride complexes of monosaccharides

The effect of stereochemistry on the complexation of aldohexoses (glucose, mannose, galactose, allose and talose) and ketohexoses (fructose, tagitose and sorbose) with transition metal chlorides (CoCl(2), NiCl(2), MnCl(2) and ZnCl(2)) has been investigated by electrospray ionization tandem mass spectrometry. Electrospray ionization of methanolic solutions of hexoses containing metal chlorides gave abundant ions corresponding to [M + MetCl](+) and [2M + MetCl](+) which on collision-induced dissociation gave characteristic fragment ions. The fragmentation pathways have been confirmed by examining methyl glucoside and several isotopically labeled glucoses. Eliminations of H(2)O and HCl, C-C cleavages and elimination of metalhydroxychloride are the competing fragmentation pathways observed. All these pathways seem to be influenced by the stereochemistry of the molecule. The fragmentation of the dimeric complexes, [2M + MetCl](+), is also controlled by the stereochemistry of the molecule. The abundance of the product ions corresponding to elimination of HCl is found to increase with increasing number of axial hydroxyl groups in aldohexoses. [2M + MetCl](+) dissociates by elimination of HCl followed by C(2)H(4)O(2) in aldohexose complexes and by elimination of HCl followed by C(3)H(6)O(3) in ketohexose complexes.     

Characterization of some synthetic Ru and Ir complexes by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) was applied to the analysis of Ru(OCOCF(3))(2)(CO)(PPh(3))(2), Ru(OCOC(3)F(7))(2)(CO)(PPh(3))(2), Ir(tBuppy)(3) and Ir(ppy)(2)(acac) complexes. A troublesome problem in the MALDI-TOFMS characterization of these metal complexes is the possible replacement of complex ligands by matrix. In this contribution, 10 matrices, ranging from acidic to basic, were investigated: alpha-cyano-4-hydroxycinnamic acid (CHCA), 2,5-dihydroxybenzoic acid (DHB), sinapinic acid (SA), dithranol, 2,4,6-trihydroxyactophenone (THAP), 6-azo-2-thiothymine (ATT), norharman, 2-[(2E)-3-(4-tert-butylphenyl)-2-methylprop-2-enylidene]malononitrile (DCTB), 4-nitroaniline (NA) and 2-amino-5-nitrophyridine (ANP). With most of the matrices, including the neutral and basic ones, matrix substitution of ligand could clearly be detected. Based on the experimental results, possible mechanisms of matrix substitution were discussed. It was demonstrated that the ligand exchange process might also occur through the gas-phase reactions initiated by laser shots. Among the matrices tested, DCTB was found to be the best one for the complexes that are prone to ligand exchange by matrix.     

Characterization of non-covalent complexes of rutin with cyclodextrins by electrospray ionization tandem mass spectrometry

Electrospray ionization tandem mass spectrometry (ESI-MS(n)) and the phase solubility method were used to characterize the gas-phase and solution-phase non-covalent complexes between rutin (R) and alpha-, beta- and gamma-cyclodextrins (CDs). The direct correlation between mass spectrometric results and solution-phase behavior is thus revealed. The order of the 1 : 1 association constants (K(c)) of the complexes between R and the three CDs in solution calculated from solubility diagrams is in good agreement with the order of their relative peak intensities and relative collision-induced dissociation (CID) energies of the complexes under the same ESI-MS(n) condition in both the positive and negative ion modes. Not only the binding stoichiometry but also the relative stabilities and even binding sites of the CD-R complexes can be elucidated by ESI-MS(n). The diagnostic fragmentation of CD-R complexes, with a significant contribution of covalent fragmentation of rutin leaving the quercetin (Q) moiety attached to the CDs, provides convincing evidence for the formation of inclusion complexes between R and CDs. The diagnostic fragment ions can be partly confirmed by the complexes between Q and CDs. The gas-phase stability order of the deprotonated CD-R complexes is beta-CD-R > alpha-CD-R > gamma-CD/R; beta-CD seems to bind R more strongly than the other CDs.     

Electrospray ionization mass spectrometry of metal complexes. Gas phase formation of a binuclear copper(II)–5-Br-PADAP complex

The complexes formed from copper(II) and 2-(5-bromo-2-pyridylazo)-5-diethylaminophenol (5-Br-PADAP or HL) in aqueous methanol solution was studied by electrospray ionization mass spectrometry. The solution of a 1:1 complex of Cu(II) with 5-Br-PADAP showed five peaks assignable to a binuclear complex [Cu₂L₂(AcO)]⁺ and mononuclear complexes [CuL]⁺, [CuL(H₂O)]⁺, [CuL(AcOH)]⁺ and [CuL(HL)]⁺ (AcO=acetate). Collision activated dissociation revealed the relative order of bonding strengths; Cu–L>Cu–HL>CuL–AcOH>CuL–H₂O. The peak intensities of the binuclear complex showed second-order dependency on those of the mono complex. As for the solution of Ni(II)–5-Br-PADAP, no binuclear complex was observed in the mass spectra. Thus, it was suggested that [Cu₂L₂(AcO)]⁺ was formed by the fast gas phase reaction: 2[CuL]⁺+AcO⁻[Cu₂L₂(AcO)]⁺.     

New algorithm for the identification of mass spectra by the computer library search

A library search algorithm for the identification of mass spectra is described. The algorithm creates the mass vector of an unknown compound spectrum and sequentially compares it with the library files vector. A measure indicating similarity of compares vectors - similarity index is calculated on the basis of weighted factors of identical elements of both vectors. A diagnosticity of vectors element defined as a function of mass distribution of library file is taken as an important parameter in similarity index calculation.     

Characterization of microchannel plate detector response for the detection of native multiply charged high mass single ions in orthogonal-time-of-flight mass spectrometry using a Timepix detector

Time-of-flight (TOF) systems are one of the most widely used mass analyzers in native mass spectrometry (nMS) for the analysis of non-covalent multiply charged bio-macromolecular assemblies (MMAs). Typically, microchannel plates (MCPs) are employed for high mass native ion detection in TOF MS. MCPs are well known for their reduced detection efficiency when impinged by large slow moving ions. Here, a position- and time-sensitive Timepix (TPX) detector has been added to the back of a dual MCP stack to study the key factors that affect MCP performance for MMA ions generated by nMS. The footprint size of the secondary electron cloud generated by the MCP on the TPX for each individual ion event is analyzed as a measure of MCP performance at each mass-to-charge (m/z) value and resulted in a Poisson distribution. This allowed us to investigate the dependency of ion mass, ion charge, ion velocity, acceleration voltage, and MCP bias voltage on MCP response in the high mass low velocity regime. The study of measurement ranges; ion mass = 195 to 802,000 Da, ion velocity = 8.4 to 67.4 km/s, and ion charge = 1+ to 72+, extended the previously examined mass range and characterized MCP performance for multiply charged species. We derived a MCP performance equation based on two independent ion properties, ion mass and charge, from these results, which enables rapid MCP tuning for single MMA ion detection.     

Studies on the non-covalent complexes between oleanolic acid and cyclodextrins using electrospray ionization tandem mass spectrometry

Non-covalent inclusion complexes formed between an anti-inflammatory drug, oleanolic acid (OA), and alpha-, beta- and gamma-cyclodextrins (CDs) were investigated by means of solubility studies and electrospray ionization tandem mass spectrometry (ESI-MS(n)). The order of calculated association constants (K(1 : 1)) of complexes between OA and different CDs in solution is in good agreement with the order of their relative peak intensities and the relative CID energies of the complexes under the same ESI-MS(n) conditions. These results indicate a direct correlation between the behaviors of solution- and gas-phase complexes. ESI-MS can thus be used to evaluate solution-phase non-covalent complexes successfully. The experimental results show that the most stable 1 : 1 inclusion complexes between three CDs and OA can be formed, but 2 : 1 CD-OA complexes can be formed with beta- and gamma-CDs. Multi-component complexes of alpha-CD-OA-beta-CD (1 : 1 : 1), alpha-CD-OA-gamma-CD (1 : 1 : 1) and beta-CD-OA-gamma-CD (1 : 1 : 1) were found in equimolar CD mixtures with excess OA. The formation of 2 : 1 and multi-component 1 : 1 : 1 non-covalent CD-OA complexes indicates that beta- and gamma-CD are able to form sandwich-type inclusion non-covalent complexes with OA. The above results can be partly supported by the relative sizes of OA and CD cavities by molecular modeling calculations. All the complexes allow the detection of gaseous deprotonated CD-OA complexes in the negative ion mode at high abundances. The relative stabilities of the CDs-OA inclusion complexes in the gas phase can be evaluated from the relative CID energies in the ion trap (alpha-CD-OA < beta-CD-OA < gamma-CD-OA) in the negative ion mode.     

Automatic recalibration and processing of tandem mass spectra using formula annotation

High accuracy, high resolution tandem mass spectrometry (MS/MS) is becoming more common in analytical applications, yet databases of these spectra remain limited. Databases require good quality spectra with sufficient compound information, but processing, calibration, noise reduction and retrieval of compound information are time‐consuming tasks that prevent many contributions. We present a comprehensive workflow for the automatic processing of MS/MS using formula annotation for recalibration and cleanup to generate high quality spectra of standard compounds for upload to MassBank ( www.massbank.jp ). Compound information is retrieved via Internet services. Reference standards of 70 pesticides were measured at various collision energies on an LTQ‐Orbitrap XL to develop and evaluate the workflow. A total of 944 resulting spectra are now available on MassBank. Evidence of nitrogen adduct formation during MS/MS fragmentation processes was found, highlighting the benefits high accuracy MS/MS offers for spectral interpretation. A database of recalibrated, cleaned‐up spectra resulted in the most correct spectra ranked in first place, regardless of whether the search spectra were recalibrated or not, whereas the average rank of the correct molecular formula was improved from 2.55 (uncalibrated) to 1.53 when using recalibrated MS/MS data. The workflow is available as an R package RMassBank capable of generating MassBank records from raw MS and MS/MS data and can be adjusted to process data acquired with different settings and instruments. This workflow is a vital step towards addressing the need for more high quality, high accuracy MS/MS spectra in spectral databases and provides important information for spectral interpretation. Copyright © 2012 John Wiley & Sons, Ltd.     

FWAVina: A novel optimization algorithm for protein-ligand docking based on the fireworks algorithm

Protein-ligand docking is an essential process that has accelerated drug discovery. How to accurately and effectively optimize the predominant position and orientation of ligands in the binding pocket of a target protein is a major challenge. This paper proposed a novel ligand binding pose search method called FWAVina based on the fireworks algorithm, which combined the fireworks algorithm with the efficient Broyden-Fletcher-Goldfarb-Shannon local search method adopted in AutoDock Vina to address the pose search problem in docking. The FWA was used as a global optimizer to rapidly search promising poses, and the Broyden-Fletcher-Goldfarb-Shannon method was incorporated into FWAVina to perform an exact local search. FWAVina was developed and tested on the PDBbind and DUD-E datasets. The docking performance of FWAVina was compared with the original Vina program. The results showed that FWAVina achieves a remarkable execution time reduction of more than 50 % than Vina without compromising the prediction accuracies in the docking and virtual screening experiments. In addition, the increase in the number of ligand rotatable bonds has almost no effect on the efficiency of FWAVina. The higher accuracy, faster convergence and improved stability make the FWAVina method a better choice of docking tool for computer-aided drug design. The source code is available at https://github.com/eddyblue/FWAVina/.     

Ruthenium coordination preferences in imidazole‐containing systems revealed by electrospray ionization mass spectrometry and molecular modeling: Possible cues for the surprising stability of the Ru (III)/tris (hydroxymethyl)‐aminomethane/imidazole complexes

Ruthenium is a platinoid that exhibits a range of unique chemical properties in solution, which are exploited in a variety of applications, including luminescent probes, anticancer therapies, and artificial photosynthesis. This paper focuses on a recently demonstrated ability of this metal in its +3 oxidation state to form highly stable complexes with tris (hydroxymethyl)aminomethane (H₂NC(CH₂OH)₃, Tris‐base or T) and imidazole (Im) ligands, where a single Ru^III cation is coordinated by two molecules of each T and Im. High‐resolution electrospray ionization mass spectrometry (ESI MS) is used to characterize Ru^III complexes formed by placing a Ru^II complex [(NH₃)₅Ru^IICl]Cl in a Tris buffer under aerobic conditions. The most abundant ionic species in ESI MS represent mononuclear complexes containing an oxidized form of the metal, ie, [X_nRu^IIIT₂ – 2H]⁺, where X could be an additional T (n = 1) or NH₃ (n = 0‐2). Di‐ and tri‐metal complexes also give rise to a series of abundant ions, with the highest mass ion representing a metal complex with an empirical formula Ru₃C₂₄O₂₁N₆H₆₆ (interpreted as cyclo(T₂RuO)₃, a cyclic oxo‐bridged structure, where the coordination sphere of each metal is completed by two T ligands). The empirical formulae of the binuclear species are consistent with the structures representing acyclic fragments of cyclo(T₂RuO)₃ with addition of various combinations of ammonia and dioxygen as ligands. Addition of histidine in large molar excess to this solution results in complete disassembly of poly‐nuclear complexes and gives rise to a variety of ionic species in the ESI mass spectrum with a general formula [Ru^IIIHis_kT_m (NH₃)_n ? 2H]⁺, where k = 0 to 2, m = 0 to 3, and n = 0 to 4. Ammonia adducts are present for all observed combinations of k and m, except k = m = 2, suggesting that [His₂Ru^IIIT₂ ? 2H]⁺ represents a complex with a fully completed coordination sphere. The observed cornucopia of Ru^III complexes formed in the presence of histidine is in stark contrast to the previously reported selective reactivity of imidazole, which interacts with the metal by preserving the RuT₂ core and giving rise to a single abundant ruthenium complex (represented by [Im₂Ru^IIIT₂ ? 2H]⁺ in ESI mass spectra). Surprisingly, the behavior of a hexa‐histidine peptide (HHHHHH) is similar to that of a single imidazole, rather than a single histidine amino acid: The RuT₂ core is preserved, with the following ionic species observed in ESI mass spectra: [HHHHHH·(Ru^IIIT₂)_m ? (3m‐1)H]⁺ (m = 1‐3). The remarkable selectivity of the imidazole interaction with the Ru^IIIT₂ core is rationalized using energetic considerations at the quantum mechanical level of theory.