Significance analysis of microarray for relative quantitation of LC/MS data in proteomics

<p>Abstract</p> <p>Background</p> <p>Although fold change is a commonly used criterion in quantitative proteomics for differentiating regulated proteins, it does not provide an estimation of false positive and false negative rates that is often desirable in a large-scale quantitative proteomic analysis. We explore the possibility of applying the Significance Analysis of Microarray (SAM) method (PNAS 98:5116-5121) to a differential proteomics problem of two samples with replicates. The quantitative proteomic analysis was carried out with nanoliquid chromatography/linear iron trap-Fourier transform mass spectrometry. The biological sample model included two <it>Mycobacterium smegmatis </it>unlabeled cell cultures grown at pH 5 and pH 7. The objective was to compare the protein relative abundance between the two unlabeled cell cultures, with an emphasis on significance analysis of protein differential expression using the SAM method. Results using the SAM method are compared with those obtained by fold change and the conventional <it>t</it>-test.</p> <p>Results</p> <p>We have applied the SAM method to solve the two-sample significance analysis problem in liquid chromatography/mass spectrometry (LC/MS) based quantitative proteomics. We grew the pH5 and pH7 unlabelled cell cultures in triplicate resulting in 6 biological replicates. Each biological replicate was mixed with a common ¹⁵N-labeled reference culture cells for normalization prior to SDS/PAGE fractionation and LC/MS analysis. For each biological replicate, one center SDS/PAGE gel fraction was selected for triplicate LC/MS analysis. There were 121 proteins quantified in at least 5 of the 6 biological replicates. Of these 121 proteins, 106 were significant in differential expression by the <it>t</it>-test (<it>p </it>< 0.05) based on peptide-level replicates, 54 were significant in differential expression by SAM with Δ = 0.68 cutoff and false positive rate at 5%, and 29 were significant in differential expression by the <it>t</it>-test (<it>p </it>< 0.05) based on protein-level replicates. The results indicate that SAM appears to overcome the false positives one encounters using the peptide-based <it>t</it>-test while allowing for identification of a greater number of differentially expressed proteins than the protein-based <it>t</it>-test.</p> <p>Conclusion</p> <p>We demonstrate that the SAM method can be adapted for effective significance analysis of proteomic data. It provides much richer information about the protein differential expression profiles and is particularly useful in the estimation of false discovery rates and miss rates.</p

MuSR method and tomographic probability representation of spin states

Muon spin rotation/relaxation/resonance (MuSR) technique for studying matter structures is considered by means of a recently introduced probability representation of quantum spin states. A relation between experimental MuSR histograms and muon spin tomograms is established. Time evolution of muonium, anomalous muonium, and a muonium-like system is studied in the tomographic representation. Entanglement phenomenon of a bipartite muon-electron system is investigated via tomographic analogues of Bell number and positive partial transpose (PPT) criterion. Reconstruction of the muon-electron spin state as well as the total spin tomography of composed system is discussed.Comment: 20 pages, 4 figures, LaTeX, submitted to Journal of Russian Laser Researc

Quark Number Susceptibility with Finite Chemical Potential in Holographic QCD

We study the quark number susceptibility in holographic QCD with a finite chemical potential or under an external magnetic field at finite temperature. We first consider the quark number susceptibility with the chemical potential. We observe that approaching the critical temperature from high temperature regime, the quark number susceptibility divided by temperature square develops a peak as we increase the chemical potential, which confirms recent lattice QCD results. We discuss this behavior in connection with the existence of the critical end point in the QCD phase diagram. We also consider the quark number susceptibility under the external magnetic field. We predict that the quark number susceptibility exhibits a blow-up behavior at low temperature as we raise the value of the magnetic field. We finally spell out some limitations of our study.Comment: 25 pages, 3 figures, published versio

Current challenges in software solutions for mass spectrometry-based quantitative proteomics

This work was in part supported by the PRIME-XS project, grant agreement number 262067, funded by the European Union seventh Framework Programme; The Netherlands Proteomics Centre, embedded in The Netherlands Genomics Initiative; The Netherlands Bioinformatics Centre; and the Centre for Biomedical Genetics (to S.C., B.B. and A.J.R.H); by NIH grants NCRR RR001614 and RR019934 (to the UCSF Mass Spectrometry Facility, director: A.L. Burlingame, P.B.); and by grants from the MRC, CR-UK, BBSRC and Barts and the London Charity (to P.C.

Search for Charged Higgs Bosons in e+e- Collisions at \sqrt{s} = 189 GeV

A search for pair-produced charged Higgs bosons is performed with the L3 detector at LEP using data collected at a centre-of-mass energy of 188.6 GeV, corresponding to an integrated luminosity of 176.4 pb^-1. Higgs decays into a charm and a strange quark or into a tau lepton and its associated neutrino are considered. The observed events are consistent with the expectations from Standard Model background processes. A lower limit of 65.5 GeV on the charged Higgs mass is derived at 95 % confidence level, independent of the decay branching ratio Br(H^{+/-} -> tau nu)

Gate-tuning of graphene plasmons revealed by infrared nano-imaging

Surface plasmons are collective oscillations of electrons in metals or semiconductors enabling confinement and control of electromagnetic energy at subwavelength scales. Rapid progress in plasmonics has largely relied on advances in device nano-fabrication, whereas less attention has been paid to the tunable properties of plasmonic media. One such medium-graphene-is amenable to convenient tuning of its electronic and optical properties with gate voltage. Through infrared nano-imaging we explicitly show that common graphene/SiO2/Si back-gated structures support propagating surface plasmons. The wavelength of graphene plasmons is of the order of 200 nm at technologically relevant infrared frequencies, and they can propagate several times this distance. We have succeeded in altering both the amplitude and wavelength of these plasmons by gate voltage. We investigated losses in graphene using plasmon interferometry: by exploring real space profiles of plasmon standing waves formed between the tip of our nano-probe and edges of the samples. Plasmon dissipation quantified through this analysis is linked to the exotic electrodynamics of graphene. Standard plasmonic figures of merits of our tunable graphene devices surpass that of common metal-based structures.Comment: 15 pages, 3 figure

Synthesis of 2-azidoethyl α-d-mannopyranoside orthogonally protected and selective deprotections

4 páginas, 1 figura, 2 esquemas.We present the synthesis of a fully orthogonally protected mannosyl glycoside 1 and the corresponding methods for selective deprotections. Mannosyl glycoside 1 contains a functionalized linker at the anomeric position to allow for the attachment of carbohydrate units to scaffolds in order to prepare carbohydrate multivalent systems.We would like to thank FIS (PI030093), for financial supportPeer reviewe