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K W Michael Siu

Publications and source records attributed to K W Michael Siu.

At least 19 recordsLinked to original sources
PubMed2007

Coordination of triply charged lanthanum in the gas phase: theory and experiment.

Ion-molecule reactions between complexes [La(CH3CN)n]3+ (n=6-9) or [La(NC(CH2)4CN)n]3+ (n=3-4) and water were studied at low collision energies in the second quadrupole of a tandem mass spectrometer. The products [La(CH3CN)p(H2O)8-p]3+ (p=6-8) and [La(NC(CH2)4CN)q(H2O)8-2q]3+ (q=3-4) had the highest relative abundances. This strongly suggests that the preferred coordination number of La3+ is eight. Similarly, the coordination number of Ca2+ was re-examined both experimentally and theoretically, and was found to be six, in good agreement with previous observations. Density functional calculations provide strong evidence that the primary solvation shell of [La(L)n]3+ consists of eight ligands; additional ligands reside in a second solvation shell and are hydrogen bonded to one or two water molecules in the first shell.

Journal Article↗
PubMed2006

Study of the enhancement of dipolar resonant excitation by linear ion trap simulations.

Resolution improvements in dipolar resonant excitation have been examined in a round-rod quadrupolar collision cell for values of the Mathieu characteristic exponent beta equal to n/p, where n and m are small integers (prime beta values) versus other beta values where n and p are not small (ordinary beta values). The trajectories of ions moving in the time-varying electric fields of a quadrupole with and without buffer-gas molecules were calculated to determine the relationship of prime and ordinary beta values to frequency resolution for resonant ion excitation and ejection. For prime beta values, the ion trajectory in the hyperbolic quadrupole field will be exactly periodic with a period of at most 4 pi p/Omega, where Omega is the angular frequency of the main drive radio-frequency (RF) potential. Ion trajectory simulations with prime beta versus ordinary beta values show that the motion of ions with prime beta values have simpler trajectories of shorter periods. Frequency response profiles (FRPs) for round-rod quadrupoles at zero pressure show that dipolar resonant excitations with prime beta values exhibit significantly narrower bandwidths than those with ordinary beta values. Simulations show that at 0.05 to 0.8 mTorr of nitrogen, it is possible to reduce the FRP bandwidth by 20% (measured at 50% depth).

Journal Article↗
PubMed2006

How large is the [Fe(III)(protoporphyrin IX)]+ ion (hemin+) in the gas phase?

Comparison of the collision cross-section of the [Fe(III)-protoporphyrin IX]+ ion, hemin+, measured by means of ion-mobility experiments and the cross-sections calculated from theoretical structures based on density functional theory reveals that hemin+, in the gas phase, contains intramolecular hydrogen bonding between its two propionic acid side-chains.

Algorithms↗
PubMed2006

The Tetrahymena thermophila phagosome proteome.

In vertebrates, phagocytosis occurs mainly in specialized cells of the immune system and serves as a primary defense against invading pathogens, but it also plays a role in clearing apoptotic cells and in tissue remodeling during development. In contrast, unicellular eukaryotes, such as the ciliate Tetrahymena thermophila, employ phagocytosis to ingest and degrade other microorganisms to meet their nutritional needs. To learn more about the protein components of the multistep process of phagocytosis, we carried out an analysis of the Tetrahymena phagosome proteome. Tetrahymena cells were fed polystyrene beads, which allowed for the efficient purification of phagosomes. The protein composition of purified phagosomes was then analyzed by multidimensional separation coupled with tandem mass spectrometry. A total of 453 peptides were identified that resulted in the identification of 73 putative phagosome proteins. Twenty-eight of the proteins have been implicated in phagocytosis in other organisms, indicating that key aspects of phagocytosis were conserved during evolution. Other identified proteins have not previously been associated with phagocytosis, including some of unknown function. Live-cell confocal fluorescence imaging of Tetrahymena strains expressing green fluorescent protein-tagged versions of four of the identified phagosome proteins provided evidence that at least three of the proteins (including two with unknown functions) are associated with phagosomes, indicating that the bulk of the proteins identified in the analyses are indeed phagosome associated.

Animals↗
PubMed2006

Fragmentations of protonated arginine, lysine and their methylated derivatives: concomitant losses of carbon monoxide or carbon dioxide and an amine.

The fragmentation pathways of protonated arginine, protonated N(alpha),N(alpha)-dimethylarginine, the N(alpha),N(alpha),N(alpha)-trimethylarginine ion, three protonated N(epsilon),N(epsilon)-dimethyllysines, and three permanent lysine ions in which the charge is fixed by trimethylation are reported. Ion assignment was facilitated by (15)N-labeling and deuterium substitution. The chemistries are dominated by charge-induced elimination of the amino groups as neutrals, including dimethylamine, trimethylamine and guanidine. Competitive losses of the alpha-amino and side-chain amino groups were observed; these losses led to intermediates that had different structures and different subsequent dissociation reactions. Concomitant losses of CO or CO(2) with these amines were also commonly observed. However, the ionic products of amine losses did not subsequently lose CO or CO(2), suggesting strongly that in these concomitant eliminations, it is the CO or CO(2) that was first eliminated, followed immediately by the loss of the amine. Results of density functional theory calculations on protonated arginine and protonated N(alpha),N(alpha)-dimethylarginine reveal that, in such concomitant eliminations, the dissociating complex is vibrationally hot and the intermediate ion formed by losing CO or CO(2) can immediately dissociate to eliminate the amine.

Amines↗
PubMed2006

Infrared multiphoton dissociation in quadrupole time-of-flight mass spectrometry: top-down characterization of proteins.

The first implementation of infrared multiphoton dissociation (IRMPD) for a hybrid quadrupole time-of-flight (QqTOF) mass spectrometer is reported. Ions were trapped in the radio frequency-only quadrupole (q2), which normally serves as a collision cell, and irradiated by a continuous CO2 IR laser. The laser beam was introduced coaxially with the quadrupoles in order to maximize overlap with the ion path. The resolution of the TOF mass analyzer allowed direct charge state determination for fragments smaller than 7 kDa. For larger fragments, the charge state could be assigned using the multiple losses of water, characteristic for IRMPD of proteins. The analytical performance is demonstrated by top-down sequencing of several representative proteins (equine myoglobin, bovine casein, and human insulin and chaperonin 10). Various post-translational modifications such as phosphorylation, acetylation, formation of disulfide bridges, and removal of N-terminal methionine followed by acetylation are detected and characterized. The utility of IRMPD for the analysis of biological samples is demonstrated in a study of a recently identified potential marker for endometrial cancer, chaperonin 10.

Amino Acid Sequence↗
PubMed2006

Stable gas-phase radical cations of dimeric tryptophan and tyrosine derivatives.

Stable radical cations of dimeric amino acid derivatives of tryptophan and tyrosine were generated by collision-induced dissociation of [Cu(II)(diethylenetriamine)(amino acid derivative)2]*2+. The yields of the dimer radical cations were dependent on both the auxiliary ligand and the tryptophan or tyrosine derivatives used. Amino acid derivatives with an unmodified carboxylic acid group did not generate dimer radical cations. For the amino acid derivatives Ac-Trp-OMe and Ac-Trp-NH2 (Ac is N-acetyl; OMe and NH2 are the methyl ester and amide modifications of the C-terminal carboxylic group), no auxiliary ligand was required for generating the dimer radical cations. Collision-induced dissociation of the [Cu(II)(amino acid derivative)4]*2+ precursor generated the dimer radical cation [(amino acid derivative)2]*+. Stabilizing interactions, most likely involving hydrogen bonding, between the two amino acid derivatives are proposed to account for observation of the dimer radical cations. Dissociation of these ions yields protonated or radical cationic amino acid derivatives; these observations are consistent with the expectation of proton competition between monomeric units, whose proton affinities were calculated using density functional theory.

Acetylation↗
PubMed2006

Gaseous bradykinin and its singly, doubly, and triply protonated forms: a first-principles study.

The conformers of gaseous bradykinin, BK, (Arg(1)-Pro(2)-Pro(3)-Gly(4)-Phe(5)-Ser(6)-Pro(7)-Phe(8)-Arg(9)) and its protonated forms, [BK + H](+), [BK + 2H](2+), and [BK + 3H](3+), were examined theoretically using a combination of the Merck molecular force field, Hartree-Fock, and density functional theory. Neutral BK, [BK + H](+), and [BK + 2H](2+) exist in zwitterionic forms that are stabilized by internal solvation and have compact structures; [BK + 3H](3+) differs by the absence of a salt bridge and adopts an elongated form. The common structural feature in all four BK species is a beta-turn in the Ser(6)-Pro(7)-Phe(8)-Arg(9) sequence. The gas-phase basicity of [BK + H](+) estimated from the calculated protonation energy is in accord with published experimental basicity; population-weighted collision cross-sections of the three ionic forms are in agreement with experimental cross-sections in the literature.

Arginine↗
PubMed2006

Characterization of the human proliferating cell nuclear antigen physico-chemical properties: aspects of double trimer stability.

Its toroidal structure allows the proliferating cell nuclear antigen (PCNA) to wrap around and move along the DNA fiber, thereby dramatically increasing the processivity of DNA polymerization. PCNA is also involved in the regulation of a wide spectrum of other biological functions, including epigenetic inheritance. We have recently reported that mammalian PCNA forms a double trimer complex, which may be critically important in coordinating DNA replication and other cellular functions. To gain a better understanding of the stability of PCNA complexes, we characterized the physico-chemical properties of the PCNA structure by in vivo and in vitro approaches. The data obtained by gel filtration and nondenaturing gel electrophoresis of native PCNA molecules confirm our previous observations, obtained using formaldehyde crosslinking, in which PCNA exists in the cell as a double trimer. We have also found that optimal pH (pH 6.5-7.5) is critical for the stability of the PCNA structure. The presence or absence of ATP, dithiothreitol, and Mg2+ does not affect the stability of the PCNA trimer or double trimer. However, 0.02% SDS can effectively inhibit PCNA double trimer, but not single trimer, formation. Interestingly, glycerol and ammonium sulfate significantly destabilize both PCNA trimer and double trimer structures.

Chromatography, Gel↗
PubMed2005

Combined ion-mobility and mass-spectrometry investigations of metallothionein complexes using a tandem mass spectrometer with a segmented second quadrupole.

Rabbit metallothionein (MT) 2A complexes with Cd(II), Zn(II), Ag(I), Cu(I), Hg(II), arsenite, monomethylarsonous acid (MMA), and dimethylarsinous acid (DMA) have been examined using ion-mobility measurements and mass spectrometry in a triple-quadrupole mass spectrometer equipped with a segmented second quadrupole that doubled as an ion-mobility cell [Guo, Y.; Wang, J.; Javahery, G.; Thomson, B. A.; Siu, K. W. M. An Ion-Mobility Spectrometer with Radial Collisional Focusing. Anal. Chem.2005, 77, 266-275]. The metal ions confer conformational rigidity on the MT complexes, which counteracts Coulombic repulsion among protons added as a result of electrospray. Triply and quadruply protonated Cd(7)MT2A have smaller cross-sections than the Cd(7)MT2A structure deduced from published NMR data. For the 6+ ions, the As(6)MT2A complex has a cross-section of 790 A(2); the MMA(10)MT2A complex, 920 A(2); and the DMA(20)MT2A complex, 1220 A(2). This increase in cross-section of the As(III) species, from As(3+) to MMA to DMA, is interpreted as a consequence of decreasing multiple coordination and increasing number of methyl groups.

Animals↗
PubMed2005

Formation of abundant [Pb(H2O)]2+ by ligand-exchange reaction between [Pb(N2)n]2+ (n = 1-3) and H2O.

Doubly charged lead monohydrate, [Pb(H2O)]2+, was predicted to be unstable in the gas phase, but it has recently been observed to form in low yield via ligand change between [Pb(CH3CN)]2+ and H2O [Shi, T.; Orlova, G.; Guo, J.; Bohme, D. K.; Hopkinson, A. C.; Siu, K. W. M. J. Am. Chem. Soc. 2004, 126, 7975-7980]. Here we report that abundant [Pb(H2O)]2+ is formed in the gas phase by ligand-exchange reaction between [Pb(N2)n]2+ (n = 1-3) and water after collisional activation. Density functional theory has been used to examine the ligand-exchange reaction profile. A comparison of the potential-energy surfaces between [Pb(N2)]2+ and [Pb(CH3CN)]2+ reacting with H2O provides strong evidence that the ligand-exchange reaction of [Pb(N2)]2+ with H2O to form [Pb(H2O)]2+ is more efficient than that of [Pb(CH3CN)]2+ with H2O.

Journal Article↗
PubMed2005

The high-pressure segmented quadrupole collision cell (HP-SQCC) as an ion molecule reactor.

A high-pressure 20-segment quadrupole collision cell (HP-SQCC), which replaces a collision cell in a modified triple-quadrupole mass spectrometer is investigated in this work as an ion-molecule reactor with an inherent heat source. The highest working pressure achievable is 20 mTorr. The 20 quadrupole segments permit superimposition of linear axial electric field over the conventional quadrupole field in the radial direction. The axial and radial fields are employed to control ion temperature. Heat is transferred to the reactants through ion frictional heating. The HP-SQCC utilizes a combination of several physicochemical phenomena and an attempt is made to examine a range of ion-molecule reactions. Due to a sufficiently large number of reactive collisions, the reactor is used to promote sequential exothermic ion-molecule reactions. To characterize the performance of the HP-SQCC, the various ion-molecule reactions between the fragment ions of ferrocene (Cp(2)Fe), cobaltocene (Cp(2)Co) and nitrogen, oxygen, water and carbon monoxide are investigated.

Journal Article↗
PubMed2005

Automated nanospray using chip-based emitters for the quantitative analysis of pharmaceutical compounds.

An automated nanospray system based on chip technology (the NanoMate) was successfully interfaced to a modified Particle Discriminator Interface on a triple quadrupole mass spectrometer. A number of the interface parameters were optimized to improve the sampling efficiency for ions from the chip-based system. Analytical performance was assessed using a number of biochemicals as well as via a methodology for a pharmaceutical that passed validation as required by Good Laboratory Practices. Infusion analyses in flow rates <1 microL/min provided advantages in terms of throughput and sample consumption when compared to other methodologies based on liquid chromatography.

Deoxycytidine↗
PubMed2005

Ion mobility spectrometer with radial collisional focusing.

An ion mobility spectrometer that has its mobility cell as a 20-segment quadrupole and functionally the q2 of a triple-quadrupole mass spectrometer has been assembled and tested. The combination of high cell pressure (maximum of 4 Torr of helium) and low axial field (20-160 V per 20.2 cm) results in negligible internal excitation of the ions despite applications of rf and axial fields. The presence of collisional focusing ensures efficient ion transmission and good sensitivity. Collision cross sections of atomic, cluster, peptide, and protein ions were measured and found comparable to literature and calculated cross sections.

Journal Article↗
PubMed2005

Proteomic analysis of the proliferative and secretory phases of the human endometrium: protein identification and differential protein expression.

Proteomic analyses of the proliferative and secretory phases of the human endometrium were carried out to identify proteins and discover differentially expressed proteins using isotope-coded affinity tags, three stages of chromatographic separation and online tandem mass spectrometry (MS/MS). From an initial list of 346 proteins identified by ProICAT, manual inspection of MS/MS spectra and confirmatory searches pared the list down to 119 positively identified proteins. Only five of the proteins showed consistent differential expression. The utility of some of these proteins as indicators of true differential expression in the endometrium is open to discussion. The two proteins with unquestionable differential expressions in the secretory endometrium are: glutamate NMDA receptor subunit zeta 1 precursor and FRAT1. Some of the proteins that show no differential expression have previously been examined in gene-expression studies with similar conclusions.

Adaptor Proteins, Signal Transducing↗
PubMed2005

A strategy for high-resolution protein identification in surface-enhanced laser desorption/ionization mass spectrometry: calgranulin A and chaperonin 10 as protein markers for endometrial carcinoma.

Surface-enhanced laser desorption/ionization-mass spectrometry (SELDI-MS) has conventionally been practiced on linear time of flight (TOF) which has low mass accuracy and resolution. Here we demonstrate in an examination of both malignant and nonmalignant endometrial tissue homogenates that high mass accuracy and resolution in the MS stage are crucial. Using a commercially available quadrupole/TOF (QqTOF), we were able to resolve two potential cancer markers, subsequently identified off-line as chaperonin 10 and calgranulin A, that differ by 8 Da in mass. Two off-line protein identification protocols were developed: the first was based on size-exclusion chromatography (SEC), sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), protein extraction, trypsin digestion, and matrix-assisted laser desorption/ionization-tandem MS (MALDI-MS/MS); the second on SEC and shotgun nano-liquid chromatography (nanoLC)-MS/MS. Analyses on a cohort of 44 endometrial homogenates showed 22 out of 23 nonmalignant samples had nondetectable to very low abundance of chaperonin 10 and calgranulin A; 17 of the 21 malignant samples had detectable to abundant levels of both proteins. Immunohistochemical staining of a tissue microarray of 32 samples showed that approximately half of malignant endometrial tissues exhibited positive staining for calgranulin A in the malignant epithelium, while 9 out of 10 benign tissues exhibited negative epithelial staining. In addition, macrophages/granulocytes in malignant as well as nonmalignant tissues showed positive staining. No immunostaining occurred in stroma or myometrium. Calgranulin A, in combination with chaperonin 10 and other proteins, may eventually constitute a panel of markers to permit diagnosis and screening of endometrial cancer.

Biomarkers, Tumor↗
PubMed2005

Direct analysis of laser capture microdissected endometrial carcinoma and epithelium by matrix-assisted laser desorption/ionization mass spectrometry.

Direct analysis of laser capture microdissected malignant and normal endometrial epithelium using matrix-assisted laser desorption/ionization (MALDI) time-of-flight mass spectrometry (MS) was able to detect a number of proteins that are overexpressed in malignant epithelial cells. A total of 16 physiologic and malignant endometrial samples were laser capture microdissected, including four proliferative and four secretory endometria, and eight endometrioid adenocarcinomas. Two of these proteins, at 10,834 and 10,843 Da, likely correspond to calgranulin A and chaperonin 10, two proteins that had previously been identified in endometrioid adenocarcinoma in whole tissue homogenate by MS analysis. Direct analysis by MALDI-MS not only confirms that these proteins are overexpressed in endometrial carcinoma, but also localizes them to the epithelial cells, the expected cancer site.

Biomarkers, Tumor↗