Incorporating In-Source Fragments Improves Metabolite Identification Accuracy in Untargeted LCMS and LCMS/MS Datasets.

In untargeted metabolomics experiments library search engines detect metabolites using several features, including precursor mass, isotopic distribution, retention time, and MS2 fragmentation. Matching acquired MS2 to library spectra is vital as numerous compounds share molecular formulas, resulting in identical precursor measurements and similar retention times. However, many metabolomics experiments are still collected using LC-MS only, and even in LC-MS/MS experiments many precursors lack MS2 spectra due to the stochastic nature of data dependent acquisition. We observe that when metabolites ionize they can produce unanticipated MS1 features resulting from neutral losses, in-source fragmentation, multimerization, and adducts. Here we present a new approach to leverage these measurements to identify metabolites when MS2 spectra are of low quality or not available. We processing datasets of 75 known standards mixed with whole yeast lysates to strip them of their MS2 scans to produce a gold-standard MS1-only data set of a complex metabolome with known targets. For each dataset we determined the proportion unambiguous annotations (where the correct annotation had a higher score than other potential annotations) and unmistakable annotations (where the correct annotation was the only valid annotation detected). We found that incorporating in-source fragments improved these metrics for both MS1-only (increasing from 60% to 73% unambiguous and 40% to 65% unmistakable matches) and MS2 datasets (from 79% to 84% unambiguous and 41% to 60% unmistakable). Unexpectedly, in these data we observed that the MS2 spectra were less useful than in-source fragment data for improving identification accuracy. We believe this is largely because the low-resolution iontrap MS2 spectra collected in this experiment show significant noise, which diminishes spectral match scores and allows other candidates to outscore the correct identifications. We suspect that noise is less likely to affect MS1 peak groups because they are generated from data aggregated across multiple high-resolution MS1 scans

Generating high quality libraries for DIA MS with empirically corrected peptide predictions.

Data-independent acquisition approaches typically rely on experiment-specific spectrum libraries, requiring offline fractionation and tens to hundreds of injections. We demonstrate a library generation workflow that leverages fragmentation and retention time prediction to build libraries containing every peptide in a proteome, and then refines those libraries with empirical data. Our method specifically enables rapid, experiment-specific library generation for non-model organisms, which we demonstrate using the malaria parasite Plasmodium falciparum, and non-canonical databases, which we show by detecting missense variants in HeLa

Interstellar Polarization in M31

The wavelength dependence of interstellar polarization due to dust in M31 has been observed along four sightlines. Only one sightline had been measured previously.The globular clusters, S78, S150, S233 and Baade 327 were used as point sources to probe the interstellar dust in M31. The Serkowski law produces good fits for all the sightlines although the relationship between K and lambda(max) may be different from that found in the Galaxy. The results of this study imply that the slope K/lambda(max) may be significantly larger in M31. The Serkowski curves are significantly narrower than those of the same lambda(max) in the Galaxy and may require extreme modifications to the size distributions of silicate particles. The fits for the four sightlines reveal values of lambda(max) ranging from 4800 to 5500 A. These are consistent with average values of lambda(max) measured in the Galaxy and the Magellanic Clouds. The range measured for M31 corresponds to R(V) values of 2.7 to 3.1. The range in R(V) seen in the Galaxy is 2.5 to 5.5 implying, for this small sample, that the average size ofinterstellar grains in M31 is typically smaller than that seen for Galactic grains if the nature of the grains is the same. Also, the polarization efficiency for these sightlines is large although some bias is expected since sightlines known to have significant interstellar polarization were selected for the sample.Comment: 13 pages, 2 figures, AJ in press (June

A Review of the Scientific Rigor, Reproducibility, and Transparency Studies Conducted by the ABRF Research Groups.

Shared research resource facilities, also known as core laboratories (Cores), are responsible for generating a significant and growing portion of the research data in academic biomedical research institutions. Cores represent a central repository for institutional knowledge management, with deep expertise in the strengths and limitations of technology and its applications. They inherently support transparency and scientific reproducibility by protecting against cognitive bias in research design and data analysis, and thedy have institutional responsibility for the conduct of research (research ethics, regulatory compliance, and financial accountability) performed in their Cores. The Association of Biomolecular Resource Facilities (ABRF) is a FASEB-member scientific society whose members are scientists and administrators that manage or support Cores. The ABRF Research Groups (RGs), representing expertise for an array of cutting-edge and established technology platforms, perform multicenter research studies to determine and communicate best practices and community-based standards. This review provides a summary of the contributions of the ABRF RGs to promote scientific rigor and reproducibility in Cores from the published literature, ABRF meetings, and ABRF RGs communications

Two Stellar Components in the Halo of the Milky Way

The halo of the Milky Way provides unique elemental abundance and kinematic information on the first objects to form in the Universe, which can be used to tightly constrain models of galaxy formation and evolution. Although the halo was once considered a single component, evidence for its dichotomy has slowly emerged in recent years from inspection of small samples of halo objects. Here we show that the halo is indeed clearly divisible into two broadly overlapping structural components -- an inner and an outer halo -- that exhibit different spatial density profiles, stellar orbits and stellar metallicities (abundances of elements heavier than helium). The inner halo has a modest net prograde rotation, whereas the outer halo exhibits a net retrograde rotation and a peak metallicity one-third that of the inner halo. These properties indicate that the individual halo components probably formed in fundamentally different ways, through successive dissipational (inner) and dissipationless (outer) mergers and tidal disruption of proto-Galactic clumps.Comment: Two stand-alone files in manuscript, concatenated together. The first is for the main paper, the second for supplementary information. The version is consistent with the version published in Natur

Anger as “seeing red”: Evidence for a perceptual association

Metaphor representation theory contends that people conceptualise their non-perceptual states (e.g., emotion concepts) in perceptual terms. The present research extends this theory to colour manipulations and discrete emotional representations. Two experiments (N=265) examined whether a red font colour would facilitate anger conceptions, consistent with metaphors referring to anger to “seeing red”. Evidence for an implicit anger-red association was robust and emotionally discrete in nature. Further, Experiment 2 examined the directionality of such associations and found that they were asymmetrical: Anger categorisations were faster when a red font colour was involved, but redness categorisations were not faster when an anger-related word was involved. Implications for multiple literatures are discussed

The genomic basis of adaptive evolution in threespine sticklebacks

Marine stickleback fish have colonized and adapted to thousands of streams and lakes formed since the last ice age, providing an exceptional opportunity to characterize genomic mechanisms underlying repeated ecological adaptation in nature. Here we develop a high-quality reference genome assembly for threespine sticklebacks. By sequencing the genomes of twenty additional individuals from a global set of marine and freshwater populations, we identify a genome-wide set of loci that are consistently associated with marine–freshwater divergence. Our results indicate that reuse of globally shared standing genetic variation, including chromosomal inversions, has an important role in repeated evolution of distinct marine and freshwater sticklebacks, and in the maintenance of divergent ecotypes during early stages of reproductive isolation. Both coding and regulatory changes occur in the set of loci underlying marine–freshwater evolution, but regulatory changes appear to predominate in this well known example of repeated adaptive evolution in nature.National Human Genome Research Institute (U.S.)National Human Genome Research Institute (U.S.) (NHGRI CEGS Grant P50-HG002568