Quantitative Mass Spectrometry Analysis Using PAcIFIC for the Identification of Plasma Diagnostic Biomarkers for Abdominal Aortic Aneurysm

BACKGROUND: Abdominal aortic aneurysm (AAA) is characterized by increased aortic vessel wall diameter (>1.5 times normal) and loss of parallelism. This disease is responsible for 1-4% mortality occurring on rupture in males older than 65 years. Due to its asymptomatic nature, proteomic techniques were used to search for diagnostic biomarkers that might allow surgical intervention under nonlife threatening conditions. METHODOLOGY/PRINCIPAL FINDINGS: Pooled human plasma samples of 17 AAA and 17 control patients were depleted of the most abundant proteins and compared using a data-independent shotgun proteomic strategy, Precursor Acquisition Independent From Ion Count (PAcIFIC), combined with spectral counting and isobaric tandem mass tags. Both quantitative methods collectively identified 80 proteins as statistically differentially abundant between AAA and control patients. Among differentially abundant proteins, a subgroup of 19 was selected according to Gene Ontology classification and implication in AAA for verification by Western blot (WB) in the same 34 individual plasma samples that comprised the pools. From the 19 proteins, 12 were detected by WB. Five of them were verified to be differentially up-regulated in individual plasma of AAA patients: adiponectin, extracellular superoxide dismutase, protein AMBP, kallistatin and carboxypeptidase B2. CONCLUSIONS/SIGNIFICANCE: Plasma depletion of high abundance proteins combined with quantitative PAcIFIC analysis offered an efficient and sensitive tool for the screening of new potential biomarkers of AAA. However, WB analysis to verify the 19 PAcIFIC identified proteins of interest proved inconclusive save for five proteins. We discuss these five in terms of their potential relevance as biological markers for use in AAA screening of population at risk

Detection of Unknown Chemical Adduct Modifications on Proteins: From Wet to Dry Laboratory

The detection and characterization of chemical adducts on proteins is of increasing interest. Here, we described a step-by-step procedure to identify unknown chemical adduct modifications on proteins resulting from the interaction with a given reactive compound. The protocol can be divided into two equally important parts: (1) the wet laboratory work, to produce high quality mass spectrometry (MS) data of in vitro modified proteins and (2) the dry laboratory work, to analyze the generated MS data and provide highly confident qualitative and quantitative results on the chemical composition and amino acid localization of adducts. This protocol is applicable to the study of any pharmaceutical or chemical compound forming covalent protein adducts, detectable in LC-MS/MS experiments

Combining bioinformatics and MS-based proteomics: clinical implications

Clinical proteomics research aims at i) discovery of protein biomarkers for screening, diagnosis and prognosis of disease, ii) discovery of protein therapeutic targets for improvement of disease prevention, treatment and follow-up, and iii) development of mass spectrometry (MS)-based assays that could be implemented in clinical chemistry, microbiology or hematology laboratories. MS has been increasingly applied in clinical proteomics studies for the identification and quantification of proteins. Bioinformatics plays a key role in the exploitation of MS data in several aspects such as the generation and curation of protein sequence databases, the development of appropriate software for MS data treatment and integration with other omics data and the establishment of adequate standard files for data sharing. In this article, we discuss the main MS approaches and bioinformatics solutions that are currently applied to accomplish the objectives of clinical proteomic research

Multiwavelength variability and correlation studies of Mrk421 during historically low X-ray and γ-ray activity in 2015–2016

In this work, we report multi-band flux variability and correlations of the nearby (z=0.031) blazar Markarian 421 (Mrk 421) using multi-wavelength (MWL) data from November 2014 to June 2016. In this period, Mrk 421 exhibited historically low activity in X-rays and very-high-energy gamma rays (VHE; E>0.1 TeV) and an additional spectral component was observed by Swift-BAT. The highest flux variability occurs in X-rays and VHE which, despite the low activity, show a significant positive correlation with no time lag. The hardness ratios in the X-rays and VHE γ-rays show the "harder-when-brighter" trend observed in many blazars. Interestingly, the trend flattens at the highest fluxes, which suggests different processes dominating the brightest states. Enlarging our data set with data from the years 2007 to 2014, we measured a positive correlation between the optical and GeV emission centered at zero time lag, and a positive correlation between the optical/GeV and the radio emission over a range of about 60 days centered at a time lag of 43+9/-6 days. This observation is consistent with the radio-bright zone being located about 0.2 parsec downstream from the optical/GeV emission regions. In most of the energy bands, the flux distribution follows the Lognormal, rather than the Normal function, indicating that the variability may be dominated by a multiplicative process

Searching for VHE gamma-ray emission associated with IceCube neutrino alerts using FACT, H.E.S.S., MAGIC, and VERITAS

The realtime follow-up of neutrino events is a promising approach to search for astrophysical neutrino sources. It has so far provided compelling evidence for a neutrino point source: the flaring gamma-ray blazar TXS 0506+056 observed in coincidence with the high-energy neutrino IceCube-170922A detected by IceCube. The detection of very-high-energy gamma rays (VHE, E>100GeV E > 100 G e V ) from this source helped establish the coincidence and constrained the modeling of the blazar emission at the time of the IceCube event. The four major imaging atmospheric Cherenkov telescope arrays (IACTs) - FACT, H.E.S.S., MAGIC, and VERITAS - operate an active follow-up program of target-of-opportunity observations of neutrino alerts sent by IceCube. This program has two main components. One are the observations of known gamma-ray sources around which a cluster of candidate neutrino events has been identified by IceCube (Gamma-ray Follow-Up, GFU). Second one is the follow-up of single high-energy neutrino candidate events of potential astrophysical origin such as IceCube-170922A. GFU has been recently upgraded by IceCube in collaboration with the IACT groups. We present here recent results from the IACT follow-up programs of IceCube neutrino alerts and a description of the upgraded IceCube GFU system

Nonresonant central exclusive production of charged-hadron pairs in proton-proton collisions at s\sqrt{s} = 13 TeV

International audienceThe central exclusive production of charged-hadron pairs in pp collisions at a centre-of-mass energy of 13\TeV is examined, based on data collected in a special high-$\beta^*$ run of the LHC. The nonresonant continuum processes are studied with the invariant mass of the centrally produced two-pion system in the resonance-free region, $m_{\pi^+\pi^-}$$\lt$ 0.7 GeV or $m_{\pi^+\pi^-}$$\gt$ 1.8 GeV. Differential cross sections as functions of the azimuthal angle between the surviving protons, squared exchanged four-momenta, and $m_{\pi^+\pi^-}$ are measured in a wide region of scattered proton transverse momenta, between 0.2 and 0.8 GeV, and for pion rapidities $\lvert y\rvert$$\lt$ 2. A rich structure of interactions related to double-pomeron exchange is observed. A parabolic minimum in the distribution of the two-proton azimuthal angle is observed for the first time. It can be interpreted as an effect of additional pomeron exchanges between the protons from the interference between the bare and the rescattered amplitudes. After model tuning, various physical quantities are determined that are related to the pomeron cross section, proton-pomeron and meson-pomeron form factors, pomeron trajectory and intercept, and coefficients of diffractive eigenstates of the proton

Nonresonant central exclusive production of charged-hadron pairs in proton-proton collisions at s\sqrt{s} = 13 TeV

International audienceThe central exclusive production of charged-hadron pairs in pp collisions at a centre-of-mass energy of 13\TeV is examined, based on data collected in a special high-$\beta^*$ run of the LHC. The nonresonant continuum processes are studied with the invariant mass of the centrally produced two-pion system in the resonance-free region, $m_{\pi^+\pi^-}$$\lt$ 0.7 GeV or $m_{\pi^+\pi^-}$$\gt$ 1.8 GeV. Differential cross sections as functions of the azimuthal angle between the surviving protons, squared exchanged four-momenta, and $m_{\pi^+\pi^-}$ are measured in a wide region of scattered proton transverse momenta, between 0.2 and 0.8 GeV, and for pion rapidities $\lvert y\rvert$$\lt$ 2. A rich structure of interactions related to double-pomeron exchange is observed. A parabolic minimum in the distribution of the two-proton azimuthal angle is observed for the first time. It can be interpreted as an effect of additional pomeron exchanges between the protons from the interference between the bare and the rescattered amplitudes. After model tuning, various physical quantities are determined that are related to the pomeron cross section, proton-pomeron and meson-pomeron form factors, pomeron trajectory and intercept, and coefficients of diffractive eigenstates of the proton

Nonresonant central exclusive production of charged-hadron pairs in proton-proton collisions at s\sqrt{s} = 13 TeV

International audienceThe central exclusive production of charged-hadron pairs in pp collisions at a centre-of-mass energy of 13\TeV is examined, based on data collected in a special high-$\beta^*$ run of the LHC. The nonresonant continuum processes are studied with the invariant mass of the centrally produced two-pion system in the resonance-free region, $m_{\pi^+\pi^-}$$\lt$ 0.7 GeV or $m_{\pi^+\pi^-}$$\gt$ 1.8 GeV. Differential cross sections as functions of the azimuthal angle between the surviving protons, squared exchanged four-momenta, and $m_{\pi^+\pi^-}$ are measured in a wide region of scattered proton transverse momenta, between 0.2 and 0.8 GeV, and for pion rapidities $\lvert y\rvert$$\lt$ 2. A rich structure of interactions related to double-pomeron exchange is observed. A parabolic minimum in the distribution of the two-proton azimuthal angle is observed for the first time. It can be interpreted as an effect of additional pomeron exchanges between the protons from the interference between the bare and the rescattered amplitudes. After model tuning, various physical quantities are determined that are related to the pomeron cross section, proton-pomeron and meson-pomeron form factors, pomeron trajectory and intercept, and coefficients of diffractive eigenstates of the proton