Microproteomic analysis of 10,000 laser captured microdissected breast tumor cells using short-range sodium dodecyl sulfate-polyacrylamide gel electrophoresis and porous layer open tubular liquid chromatography tandem mass spectrometry

Precise proteomic profiling of limited levels of disease tissue represents an extremely challenging task. Here, we present an effective and reproducible microproteomic workflow for sample sizes of only 10,000 cells that integrates selective sample procurement via laser capture microdissection (LCM), sample clean-up and protein level fractionation using short-range SDS-PAGE, followed by ultrasensitive LC-MS/MS analysis using a 10 μm i.d. porous layer open tubular (PLOT) column. With 10,000 LCM captured mouse hepatocytes for method development and performance assessment, only 10% of the in-gel digest, equivalent to ～1000 cells, was needed per LC-MS/MS analysis. The optimized workflow was applied to the differential proteomic analysis of 10,000 LCM collected primary and metastatic breast cancer cells from the same patient. More than 1100 proteins were identified from each injection with >1700 proteins identified from three LCM samples of 10,000 cells from the same patient (1123 with at least two unique peptides). Label free quantitation (spectral counting) was performed to identify differential protein expression between the primary and metastatic cell populations. Informatics analysis of the resulting data indicated that vesicular transport and extracellular remodeling processes were significantly altered between the two cell types. The ability to extract meaningful biological information from limited, but highly informative cell populations demonstrates the significant benefits of the described microproteomic workflow.     

Simultaneous determination of perfluoroalkyl phosphonates, carboxylates, and sulfonates in drinking water

A trace analytical method based on high performance liquid chromatography coupled to quadrupole time-of-flight high resolution mass spectrometry was developed for simultaneous determination of perfluoroalkyl phosphonates (PFPAs, carbon chain lengths C6,8,10), perfluoroalkyl carboxylates (PFCAs, C5-12), and perfluoroalkyl sulfonates (PFSAs, C4,6,8,10) in drinking water (tap water). Analytes were enriched on a mixed mode co-polymeric sorbent (C8+quaternary amine) using solid phase extraction. Chromatographic separation was achieved on a Zorbax Extend C18 reversed phase column using a mobile phase gradient consisting of water, methanol, and acetonitrile containing 2mM ammonium acetate and 5 mM 1-methyl piperidine. The mass spectrometer was operated in electrospray negative ion mode. Use of 1-methyl piperidine in the mobile phase resulted in a significant increase in instrument sensitivity for PFPAs through improved chromatographic resolution, background suppression, and increased ionization efficiency. Method detection limits for extraction of 500 mL tap water were in the ranges of 0.095-0.17 ng/L, 0.027-0.17 ng/L, and 0.014-0.052 ng/L for PFPAs, PFCAs, and PFSAs, respectively. Whole method recoveries at a spiking level of 0.5 ng/L to 500 mL HPLC grade water were 40-56%, 56-97%, and 55-77% for PFPAs, PFCAs, and PFSAs, respectively. A matrix effect (signal enhancement) was observed in the detection of PFPAs in tap water extracts, leading to calculated recoveries of 249-297% at a 0.5 ng/L spiking level. This effect resulted in an additional improvement of method sensitivity for PFPAs. To compensate for the matrix effect, PFPAs in tap water were quantified using matrix-matched and extracted calibration standards. The method was successfully applied to the analysis of drinking water collected from six European countries. PFPAs were not detected except for perfluorooctyl phosphonate (PFOPA) at close to the detection limit of 0.095 ng/L in two water samples from Amsterdam, the Netherlands. Highest levels were found for perfluorobutane sulfonate (PFBS, 18.8 ng/L) and perfluorooctanoate (PFOA, 8.6 ng/L) in samples from Amsterdam as well as for perfluorooctane sulfonate (PFOS, 8.8 ng/L) in tap water from Stockholm, Sweden.     

Understanding the complex dissociation dynamics of energy selected dichloroethylene ions: neutral isomerization energies and heats of formation by imaging photoelectron-photoion coincidence

The dissociative photoionization of 1,1-C(2)H(2)Cl(2), (E)-1,2-C(2)H(2)Cl(2), and (Z)-1,2-C(2)H(2)Cl(2) has been investigated at high energy and mass resolution using the imaging photoelectron photoion coincidence instrument at the Swiss Light Source. The asymmetric Cl-atom loss ion time-of-flight distributions were fitted to obtain the dissociation rates in the 10(3) s(-1) < k < 10(7) s(-1) range as a function of the ion internal energy. The results, supported by ab initio calculations, show that all three ions dissociate to the same C(2v) symmetry ClC═CH(2)(+) product ion. The 0 K onset energies thus establish the relative heats of formation of the neutral isomers, that is, the isomerization energies. The experimental rate constants, k(E), as well as ab initio calculations indicate an early isomerization transition state and no overall reverse barrier to dissociation. The major high energy channels are the parallel HCl loss and the sequential ClC═CH(2)(+) → HCCH(+) + Cl process, the latter in competition with a ClC═CH(2)(+) → ClCCH(+) + H reaction. A parallel C(2)H(2)Cl(2)(+) → C(2)HCl(2)(+) + H channel also weakly asserts itself. The 0 K onset energy for the sequential Cl loss reaction suggests no barrier to the production of the most stable acetylene ion product; thus the sequential Cl-atom loss is preceded by a ClC═CH(2)(+) → HC(Cl)CH(+) reorganization step with a barrier lower than that of the second Cl-atom loss. The breakdown diagram corresponding to this sequential dissociation reveals the internal energy distribution of the first C(2)H(2)Cl(+) daughter ion, which is determined by the kinetic energy release in the first, Cl loss reaction at high excess energies. At low kinetic energy release, this distribution corresponds to the predicted two translational degrees of freedom, whereas at higher energies, the excess energy partitioning is characteristic of only one translational degree of freedom. New Δ(f)H(o)(298K) of 3.7, 2.5, and 0.2 ± 1.75 kJ mol(-1) are proposed for 1,1-C(2)H(2)Cl(2), (E)-1,2-C(2)H(2)Cl(2), and (Z)-1,2-C(2)H(2)Cl(2), respectively, and the proton affinity of ClCCH is found to be 708.6 ± 2.5 kJ mol(-1).     

Biotransformation of (1S)-2-carene and (1S)-3-carene by Picea abies suspension culture

Biotransformation of (1S)-2-carene and (1S)-3-carene by Picea abies suspension culture led to the formation of oxygenated products. (1S)-2-Carene was transformed slowly and the final product was identified as (1S)-2-caren-4-one. On the other hand, the transformation of (1S)-3-carene was rapid and finally led to the formation of (1S)-3-caren-5-one and (1S)-2-caren-4-one as equally abundant major products. The time-course of the reaction indicates that some products abundant at the beginning of the reaction (e.g. (1S, 3S, 4R)-3,4-epoxycarane and (1R)-p-mentha-1(7),2-dien-8-ol) were consumed by a subsequent transformations. Thus, a precise selection of the biotransformation time may be used for a production of specific compounds.     

Major elements as possible factors of trace element urban pedochemical anomalies

The relationship between real total contents of the major elements Na, Mg, Al, Si, P, S, K, Ca, Ti, Fe and the trace elements Ag, As, B, Ba, Co, Cr, Cu, Mn, Mo, Ni, Pb, Sb, Se, Sn, V, U, Zn in topsoil from the central part of Vilnius is analysed. The amounts of most elements were determined by energy-dispersive X-ray fluorescence, while amounts of Ag, B, Co were measured by optical atomic emission spectrophotometry. Two factors were distinguished according to major elements: anthropogenic (A) including Ca, Mg, Fe, P, S and clayey (C) including K, Al, Ti. Boron, Mn, Cr and U are significantly correlated with members of both factors, Sb with none of them and other trace elements either with all (Cu, Zn, Pb, Se, Ba, Ni, Co) or with separate (V, Ag, Sn, Mo, As) members of the A-factor. Only B, Mn, Cr, U (partly their additive index Z1) are influenced by the C-factor, while twelve other trace elements (also their additive index Z2) are influenced by the A-factor. The additive index Z of all 17 elements is also affected by the A-factor. Four groups of sites have been distinguished according to normal or higher contents of both factors. The majority of trace element anomalies are related to the sites affected by the A-factor.     

Selected bibliography on degeneracy

A selected bibliography on degeneracy problems organized according to the appearance of the respective references in various fields of operations research is given.     

Electronic structure and electron dynamics at the GaSb(0 0 1) surface studied by femtosecond pump-and-probe pulsed laser photoemission spectroscopy

Transiently excited electron states at the GaSb(0 0 1) surface have been studied by means of time- and angle-resolved photoemission spectroscopy based on a femtosecond laser system. A normally unpopulated surface electron state has been found at ∼250 meV above the valence band maximum with a strong confinement at the center of the surface Brillouin zone. The lifetime of transiently excited carriers at the intergap surface states has been found to be ∼11 ps, associated with rapid carrier diffusion.     

A new diquark model for deep inelastic structure functions

The bulk of data from deep inelasticep, eD, μp, μN, νp and νN scattering is fitted with a new diquark model of nucleons. The proton is found to be mostly in au(ud) ₀ state, where the (ud)₀ diquark has spin and isospin zero. There is hence no trace ofSU(6) symmetry among diquarks in nucleons.