Ion mobility mass spectrometry: an elegant alternative focusing on speciation studies

This work is proposed to demonstrate the Traveling-Wave Ion Mobility Specrometry (TWIMS) coupled to Mass Spectrometry (MS) as an alternative technique for speciation analysis between metals/metalloids and biomolecules. Mobilities of bovine carbonic anhydrase bound to Ba(2+), Cu(2+), Pb(2+), Zn(2+), Cr(3+), Cr(6+), Se(4+) and Se(6+) were estimated. The metal belonging to the bovine carbonic anhydrase structure, commonly found in the commercially available enzyme, was removed by filtration, using centrifugal filter devices. Then, some metals/metalloids were added to 10.0 mmol L(-1) ammonium acetate at pH = 6.8 enzyme solution. Experiments were carried out by direct insertion of the sample at 10 mu L min(-1) flow rate into the ESI source of the instrument. Carbonic anhydrase mobility varied according to the metal bound in its structure, following the order: Zn(2+) < Cu(2+) < Ba(2+) < Pb(2+). Metals with higher affinity by the enzyme, such as Zn(2+) and Cu(2+) had lower mobility, suggesting a higher structural modification, binding itself to the enzyme metallic site. Considering metals with different oxidation states, the enzyme mobility followed the order: Se(4+) < Cr(6+) < Se(6+) < Cr(3+).26120120

Organoindate room temperature ionic liquid: Synthesis, physicochemical properties and application

The combination of equimolar amounts of solid 1-n-butyl-3-methylimidazolum chloride (BMI-Cl) with solid indium trichloride affords the new room temperature and air stable ionic liquid BMI.InCl4 (mp -6 degreesC). The major physicochemical properties (density, viscosity, electrical conductivity and electrochemical window) of BMI.InCl4 are complementary to those of classical tetrafluoroborate or hexafluorophosphate analogues. However, this liquid possesses similar Lewis acidity properties to those of organoaluminate melts and can be used as recyclable media, as demonstrated here for the tetrahydropyranylation of alcohols.81155115

2-pyridyl and 2-pyrimidyl cations: Stable o-hetarynium ions in the gas phase

As indicated by high-level CBS-Q ab initio calculations, extensive overlap occurs in the 2-pyridyl and 2-pyrimidyl cations between the fully occupied sp(2) orbital of nitrogen and the adjacent, coplanar, and empty spl orbital of the C2-carbon. Such effective orbital overlap results in o-aryne-like structures with substantially shorter N-C+ bond lengths and N-C+ bond orders of 1.9-2.1. Therefore. the 2-pyridyl and 2-pyrimidyl cations are best represented, and can be regarded as, o-hetarynium ions, being more stable than their positional, nonconjugated isomers by as much as 18-28 kcal/mol. The 4-pyrimidyl cation also displays characteristic o-hetarynium ion structure with substantial orbital overlap. However, the ion easily isomerizes by charge-induced ring opening, as indicated by both the calculations and the ion's lack of o-hetarynium-like reactivity. A high energy barrier of 62.8 kcal/mol hampers isomerization by H-ring walking of the 3-pyridyl cation to the far more stable 2-pyridyl cation. For the related 2-furanyl, 2-thiophenyl, and 2-pyrrolyl cations, little or none of the extra orbital overlap occurs; hence, they display energies close, and structures similar, to those of their 3-isomers. Collision-induced dissociation of collisionally quenched precursor ions performed via triple-stage QqQqQ mass spectrometric (MSS) experiments confirms the greater stability of the 2-pyridyl and 2-pyrimidyl cations.6472188219

THE ISOMERS OF IONIZED DIMETHYL-SULFOXIDE (C2H6OS+.) AND THEIR CH3OS+ FRAGMENTS - AN AB-INITIO AND MULTIPLE-STAGE MASS-SPECTROMETRIC (MS(N)) STUDY

The relative stabilities, isomerizations and dissociations of ionized dimethyl sulfoxide (DMSO), its three C2H6OS+. isomers and of all their 14 conceivable CH3OS+ fragments (1-14), have been investigated by ab initio calculations at the MP2/6-31G(d,p)//6-31G(d,p) + ZPE and G2 levels of theory, and by multiple-stage two- and three-dimensional mass spectrometry performed in a pentaquadrupole instrument. The ab initio relative energies of the isomers, their connecting transition states, and their dissociation thresholds were used to elaborate potential energy surface diagrams that precisely corroborate and unify several previously divergent experimental observations on these systems. The most kinetically favorable isomerization of (CH3)(2)-S=O-+. (I) to its aci-form CH2=S(OH)-CH3+. (II) displays a transition state considerably lower in energy than the threshold for its direct dissociation by CH3. loss. Therefore, low-energy, long-lived metastable ions I are predicted to isomerize to II, and to dissociate in turn to CH2=S+-OH (2) upon CH3. loss. Ions I excited a few electronvolts above the threshold are, on the other hand, predicted to dissociate directly to CH3-S+-O (1). Isomerization of I to the most stable C2H6OS+. isomers, that is 1, 2, (H-CS ... OH2)(+) (3), (CH2)-C-+-S(=O)H (4), 5, HC(=SH)OH+ (9), CH2-O-SH+ (10), CH2+-O-SH (11), and (H-CO ... SH2)(+) (14), were found as true minima on the RHF/6-31G(d,p) potential-energy surface, and some of their isomerization barriers and dissociation thresholds were estimated. Tandem and multiple-stage (MS(3)) mass spectrometric experiments show that non-dissociating DMSO(+.) ions produce, upon collision-induced dissociation (CID), a mixture of approximately 40% of 1 and 60% of 2, whereas the CID chemistry of 1 and 2 is affected considerably by the collision energies employed. Both the experimental and theoretical results on 1 and 2 allow a detailed interpretation of their complex dissociation chemistry, which clarifies the nature of most of their indirect fragments. Such fragments are proposed to be formed via the common isomerization/dissociation sequences 1 --> 2 --> 9 reversible arrow 3 --> HCS+ (m/z 45) + H2O, and 1 --> 2 --> [7, HO-CH2-S+] --> S+CH2OH+ (m/z 31). These processes are favored at lower collision energies, whereas direct dissociation of 1 to CH3+ (m/z 15) and SO+. (m/z 48), and of 2 to CH2S+. (m/z 46) occurs to greater extents at higher collision energies.30111553156

Primary and secondary kinetic isotope effects in proton (H+/D+) and chloronium ion (35Cl(+)/37Cl(+)) affinities

The Cooks' kinetic method and tandem-in-space pentaquadrupole QqQqQ mass spectrometry were used to measure primary and secondary kinetic isotope effects (KIEs) in H+ and Cl+ (X+) affinity for a series of A/A' isotopomeric pairs. Gaseous, isotopomeric, and loosely bound dimers [A...chi (+)...A] were formed in combinations in which chi = H+, D+, Cl-35(+) or Cl-37(+) and A/A' = acetonitrile/acetonitrile-d(3), acetonitrile/acetonitrile-N-15, acetonitrile-d(3)/acetonitrile-N-15, acetone/acetone-d(6), acetone/acetone-O-18, acetone-d(6)/acetone-O-18, pyridine/pyridine-d(5), pyridine/pyridine-N-15, pyridine-d(5)/pyridine-N-15, or 3-(Cl-35)chloropyridine/3-(Cl-37) chloropyridine. Under nearly the same experimental conditions, the dimers were mass-selected and then dissociated by low-energy collisions with argon, yielding AX(+) and A'X+ as the fragment ions. KIEs were measured from the changes in ion affinities of the neutrals (AXI) as estimated by the AX(+)/A'X+ abundance ratios. Using [A...H+(D+)... '] and [A...Cl-35(+)(Cl-37(+))...A'] dimers and by comparing their extent of dissociation tinder nearly identical collision-induced dissociation conditions, the kinetic method was also applied, for the first time, to measure primary KIEs of the central ion as well as their influence on secondary KIEs. Becke3LYP/6311++G(2df,2p) calculations were found to provide Delta(Delta ZPE)s for the competitive dissociation reactions that accurately predict the nature (normal or inverse) of the measured KIEs. Copyright (C) 2001 John Wiley & Sons, Ltd.36101140114

Chemical cross-linking with a diazirine photoactivatable cross-linker investigated by MALDI- and ESI-MS/MS

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Crystallography and nuclear magnetic resonance are well-established methods to study protein tertiary structure and interactions. Despite their usefulness, such methods are not applicable to many protein systems. Chemical cross-linking of proteins coupled with mass spectrometry allows low-resolution characterization of proteins and protein complexes based on measuring distance constraints from cross-links. In this work, we have investigated cross-linking by means of a heterobifunctional cross-linker containing a traditional N-hydroxysuccinimide (NHS) ester and a UV photoactivatable diazirine group. Activation of the diazirine group yields a highly reactive carbene species, with potential to increase the number of cross-links compared with homobifunctional, NHS-based cross-linkers. Cross-linking reactions were performed on model systems such as synthetic peptides and equine myoglobin. After reduction of the disulfide bond, the formation of intra- and intermolecular cross-links was identified and the peptides modified with both NHS and diazirine moieties characterized. Fragmentation of these modified peptides reveals the presence of a marker ion for intramolecular cross-links, which facilitates identification. Copyright (c) 2010 John Wiley & Sons, Ltd.458892899Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)FAPESP [FAPESP 2004/14846-0, FINEP 01 07 0290.00]FAPESP [FAPESP 08/57805-2, CNPq 573672/2008-3

Fragmentation features of intermolecular cross-linked peptides using N-hydroxy-succinimide esters by MALDI- and ESI-MS/MS for use in structural proteomics

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)The use of mass spectrometry coupled with chemical cross-linking of proteins has become one of the most useful tools for proteins structure and interactions studies. One of the challenges in these studies is the identification of the cross-linked peptides. The interpretation of the MS/MS data generated in cross-linking experiments using N-hydroxy succinimide esters is not trivial once a new amide bond is formed allowing new fragmentation pathways, unlike linear peptides. Intermolecular cross-linked peptides occur when two different peptides are connected by the cross-linker and they yield information on the spatial proximity of different domains (within a protein) or proteins (within a complex). In this article, we report a detailed fragmentation study of intermolecular cross-linked peptides, generated from a set of synthetic peptides, using both ESI and MAID! to generate the precursor ions. The fragmentation features observed here can be helpful in the interpretation and identification of cross-linked peptides present in cross-linking experiments and be further implemented in search engine's algorithms. Copyright (C) 2011 John Wiley & Sons, Ltd.468742750Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)FAPESP [FAPESP 2004/14846-0, FINEP 01.07.0290.00]FAPESP [CNPq 573672/2008-3, FAPESP 08/57805-2]FAPESP [2007/55930-1

IRMPD and ECD fragmentation of intermolecular cross-linked peptides

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Despite the increasing number of studies using mass spectrometry for three dimensional analyses of proteins (MS3D), the identification of cross-linked peptides remains a bottleneck of the method. One of the main reasons for this is the lack of knowledge about the fragmentation of these species. Intermolecular cross-linked peptides are considered the most informative species present in MS3D experiment, since different peptides are connected by a cross-linker, the peptides chain can be either from a single protein, providing information about protein folding, or from two different proteins in a complex, providing information about binding partners, complex topology and interaction sites. These species tend to be large and highly charged in ESI, making comprehensive fragmentation by CID MS/MS problematic. On the other hand, these highly charged peptides are very suitable for dissociation using both infrared multiphoton dissociation (IRMPD) and electron capture dissociation (ECD). Herein, we report the fragmentation study of intermolecular cross-linked peptides using IRMPD and ECD. Using synthetic peptides and different commercial cross-linkers, a series of intermolecular cross-linked peptides were generate, and subsequently fragmented by IRMPD and ECD in a FT-ICR-MS instrument. Due to the high mass accuracy and resolution of the FT-ICR, the fragment ions could be attributed with high confidence. The peptides sequence coverage and fragmentation features obtained from IRMPD and ECD were compared for all charge states. Copyright (C) 2011 John Wiley & Sons, Ltd.463262268Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)FAPESP [FAPESP 2004/14846-0, FINEP 01.07.0290.00]FAPESP [FAPESP 08/57805-2, CNPq 573672/2008-3