Spectral counting assessment of protein dynamic range in cerebrospinal fluid following depletion with plasma-designed immunoaffinity columns

<p>Abstract</p> <p>Background</p> <p>In cerebrospinal fluid (CSF), which is a rich source of biomarkers for neurological diseases, identification of biomarkers requires methods that allow reproducible detection of low abundance proteins. It is therefore crucial to decrease dynamic range and improve assessment of protein abundance.</p> <p>Results</p> <p>We applied LC-MS/MS to compare the performance of two CSF enrichment techniques that immunodeplete either albumin alone (IgYHSA) or 14 high-abundance proteins (IgY14). In order to estimate dynamic range of proteins identified, we measured protein abundance with APEX spectral counting method.</p> <p>Both immunodepletion methods improved the number of low-abundance proteins detected (3-fold for IgYHSA, 4-fold for IgY14). The 10 most abundant proteins following immunodepletion accounted for 41% (IgY14) and 46% (IgYHSA) of CSF protein content, whereas they accounted for 64% in non-depleted samples, thus demonstrating significant enrichment of low-abundance proteins. Defined proteomics experiment metrics showed overall good reproducibility of the two immunodepletion methods and MS analysis. Moreover, offline peptide fractionation in IgYHSA sample allowed a 4-fold increase of proteins identified (520 vs. 131 without fractionation), without hindering reproducibility.</p> <p>Conclusions</p> <p>The novelty of this study was to show the advantages and drawbacks of these methods side-to-side. Taking into account the improved detection and potential loss of non-target proteins following extensive immunodepletion, it is concluded that both depletion methods combined with spectral counting may be of interest before further fractionation, when searching for CSF biomarkers. According to the reliable identification and quantitation obtained with APEX algorithm, it may be considered as a cheap and quick alternative to study sample proteomic content.</p

First search for a dark matter annual modulation signal with NaI(Tl) in the Southern Hemisphere by DM-Ice17

We present the first search for a dark matter annual modulation signal in the Southern Hemisphere conducted with NaI(Tl) detectors, performed by the DM-Ice17 experiment. Nuclear recoils from dark matter interactions are expected to yield an annually modulated signal independent of location within the Earth’s hemispheres. DM-Ice17, the first step in the DM-Ice experimental program, consists of 17 kg of NaI(Tl) located at the South Pole under 2200 m.w.e. overburden of Antarctic glacial ice. Taken over 3.6 years for a total exposure of 60.8 kg yr, DM-Ice17 data are consistent with no modulation in the energy range of 4–20 keV, providing the strongest limits on weakly interacting massive particle dark matter from a direct detection experiment located in the Southern Hemisphere. The successful deployment and stable long-term operation of DM-Ice17 establishes the South Pole ice as a viable location for future dark matter searches and in particular for a high-sensitivity NaI(Tl) dark matter experiment to directly test the DAMA/LIBRA claim of the observation of dark matter

Mass spectrometry-based absolute quantification of 20S proteasome status for controlled ex-vivo expansion of Human Adipose-derived Mesenchymal Stromal/Stem Cells

The proteasome controls a multitude of cellular processes through protein degradation and has been identified as a therapeutic target in oncology. However, our understanding of its function and the development of specific modulators are hampered by the lack of a straightforward method to determine the overall proteasome status in biological samples. Here, we present a method to determine the absolute quantity and stoichiometry of ubiquitous and tissue-specific human 20S proteasome subtypes based on a robust, absolute SILAC-based multiplexed LC-Selected Reaction Monitoring (SRM) quantitative mass spectrometry assay with high precision, accuracy, and sensitivity. The method was initially optimized and validated by comparison with a reference ELISA assay and by analyzing the dynamics of catalytic subunits in HeLa cells following IFNγ-treatment and in range of human tissues. It was then successfully applied to reveal IFNγ- and O2-dependent variations of proteasome status during primary culture of Adipose-derived-mesenchymal Stromal/Stem Cells (ADSCs). The results show the critical importance of controlling the culture conditions during cell expansion for future therapeutic use in humans. We hypothesize that a shift from the standard proteasome to the immunoproteasome could serve as a predictor of immunosuppressive and differentiation capacities of ADSCs and, consequently, that quality control should include proteasomal quantification in addition to examining other essential cell parameters. The method presented also provides a new powerful tool to conduct more individualized protocols in cancer or inflammatory diseases where selective inhibition of the immunoproteasome has been shown to reduce side effects

Muon detector for the COSINE-100 experiment

The COSINE-100 dark matter search experiment has started taking physics data with the goal of performing an independent measurement of the annual modulation signal observed by DAMA/LIBRA. A muon detector was constructed by using plastic scintillator panels in the outermost layer of the shield surrounding the COSINE-100 detector. It detects cosmic ray muons in order to understand the impact of the muon annual modulation on dark matter analysis. Assembly and initial performance tests of each module have been performed at a ground laboratory. The installation of the detector in the Yangyang Underground Laboratory (Y2L) was completed in the summer of 2016. Using three months of data, the muon underground flux was measured to be 328 ± 1(stat.)± 10(syst.) muons/m2/day. In this report, the assembly of the muon detector and the results from the analysis are presented

Initial performance of the COSINE-100 experiment

COSINE is a dark matter search experiment based on an array of low background NaI(Tl) crystals located at the Yangyang underground laboratory. The assembly of COSINE-100 was completed in the summer of 2016 and the detector is currently collecting physics quality data aimed at reproducing the DAMA/LIBRA experiment that reported an annual modulation signal. Stable operation has been achieved and will continue for at least 2 years. Here, we describe the design of COSINE-100, including the shielding arrangement, the configuration of the NaI(Tl) crystal detection elements, the veto systems, and the associated operational systems, and we show the current performance of the experiment

Background model for the NaI(Tl) crystals in COSINE-100

The COSINE-100 dark matter search experiment is an array of NaI(Tl) crystal detectors located in the Yangyang Underground Laboratory (Y2L). To understand measured backgrounds in the NaI(Tl) crystals we have performed Monte Carlo simulations using the Geant4 toolkit and developed background models for each crystal that consider contributions from both internal and external sources, including cosmogenic nuclides. The background models are based on comparisons of measurement data with Monte Carlo simulations that are guided by a campaign of material assays and are used to evaluate backgrounds and identify their sources. The average background level for the six crystals (70 kg total mass) that are studied is 3.5 counts/day/keV/kg in the (2–6) keV energy interval. The dominant contributors in this energy region are found to be 210Pb and 3H

The COSINE-100 data acquisition system

COSINE-100 is a dark matter direct detection experiment designed to test the annual modulation signal observed by the DAMA/LIBRA experiment. COSINE-100 consists of 8 NaI(Tl) crystals with a total mass of 106 kg, a 2200 L liquid scintillator veto, and 37 muon detector panels. We present details of the data acquisition system of COSINE-100, including waveform storage using flash analog-to-digital converters for crystal events and integrated charge storage using charge-sensitive analog-to-digital converters for liquid scintillator and plastic scintillator muon veto events. We also discuss several trigger conditions developed in order to distinguish signal events from photomultiplier noise events. The total trigger rate observed for the crystal/liquid scintillator (plastic scintillator) detector is 15 Hz (24 Hz)

Search for a dark matter-induced annual modulation signal in NaI(Tl) with the COSINE-100 experiment

We present new constraints on the dark matter-induced annual modulation signal using 1.7\,years, of COSINE-100 data with a total exposure of 97.7\,kg⋅years. The COSINE-100 experiment, consisting of 106\,kg of NaI(Tl) target, is designed to carry out a model-independent test of DAMA/LIBRA's claim by searching for the same annual modulation signal using the same NaI(Tl) target. The crystal data show 2.7 counts/keV/kg/day background rate on average in the 2--6 keV energy region of interest. Using a chi-squared minimization method we observe best fit values for modulation amplitude and phase at 0.0092±0.0067 counts/keV/kg/day and 127.2±45.9 days, respectively