Wood Fall Data and Species List

Wood Fall Data and Species Lis

R Script for Wood Fall Analyses

R Script for Wood Fall Analyse

Atlantic Deep-Sea Bivalves

Biogeographic and ecological data for deep-sea bivalves. Location data based on Allen (2008). Read McClain et al. (2011) for more details (doi: 10.1098/rspb.2011.2166

Ecological modes of fossil bivalve genera

This data set contains ecological modes of life assigned to fossil bivalve genera with stage-level resolution first and last appearance dates

Data Dependent Peak Model Based Spectrum Deconvolution for Analysis of High Resolution LC-MS Data

A data dependent peak model (DDPM) based spectrum deconvolution method was developed for analysis of high resolution LC-MS data. To construct the selected ion chromatogram (XIC), a clustering method, the density based spatial clustering of applications with noise (DBSCAN), is applied to all <i>m</i>/<i>z</i> values of an LC-MS data set to group the <i>m</i>/<i>z</i> values into each XIC. The DBSCAN constructs XICs without the need for a user defined <i>m</i>/<i>z</i> variation window. After the XIC construction, the peaks of molecular ions in each XIC are detected using both the first and the second derivative tests, followed by an optimized chromatographic peak model selection method for peak deconvolution. A total of six chromatographic peak models are considered, including Gaussian, log-normal, Poisson, gamma, exponentially modified Gaussian, and hybrid of exponential and Gaussian models. The abundant nonoverlapping peaks are chosen to find the optimal peak models that are both data- and retention-time-dependent. Analysis of 18 spiked-in LC-MS data demonstrates that the proposed DDPM spectrum deconvolution method outperforms the traditional method. On average, the DDPM approach not only detected 58 more chromatographic peaks from each of the testing LC-MS data but also improved the retention time and peak area 3% and 6%, respectively

Data Preprocessing Method for Liquid Chromatography–Mass Spectrometry Based Metabolomics

A set of data preprocessing algorithms for peak detection and peak list alignment are reported for analysis of liquid chromatography–mass spectrometry (LC–MS)-based metabolomics data. For spectrum deconvolution, peak picking is achieved at the selected ion chromatogram (XIC) level. To estimate and remove the noise in XICs, each XIC is first segmented into several peak groups based on the continuity of scan number, and the noise level is estimated by all the XIC signals, except the regions potentially with presence of metabolite ion peaks. After removing noise, the peaks of molecular ions are detected using both the first and the second derivatives, followed by an efficient exponentially modified Gaussian-based peak deconvolution method for peak fitting. A two-stage alignment algorithm is also developed, where the retention times of all peaks are first transferred into the <i>z</i>-score domain and the peaks are aligned based on the measure of their mixture scores after retention time correction using a partial linear regression. Analysis of a set of spike-in LC–MS data from three groups of samples containing 16 metabolite standards mixed with metabolite extract from mouse livers demonstrates that the developed data preprocessing method performs better than two of the existing popular data analysis packages, MZmine2.6 and XCMS², for peak picking, peak list alignment, and quantification

List of triacylglycerols in liver identified with significant concentration changes between the control cohort and the test cohort at two and four weeks.

a<p>Fold-change is the ratio of average peak area of a metabolite in the test cohort (T) to that in the control cohort (C).</p>b<p>na refers to a metabolite that was detected only in the test cohort. Therefore, the values of fold change for these metabolites are not available.</p

Time course changes of WAT tissues.

<p>(A) WAT mass. The weights of both eWAT and sWAT in control mice increased gradually during the 4 weeks of experiment. However, the alcohol-fed mice did not show weight change in both eWAT and sWAT at either 2 weeks or 4 weeks. (B) WAT to body weight ratio (%). Data are expressed as mean ± SD (<i>n</i> = 6−8). Statistical differences were analyzed by ANOVA followed by Bonferroni <i>post hoc</i> comparison, and means without a common letter differ at <i>p</i><0.05.</p

Time course trajectory of triacylglycerol TG(16∶0/18∶2/20∶4)[iso6] without any deuterium labeling in liver samples.

<p>Time course trajectory of triacylglycerol TG(16∶0/18∶2/20∶4)[iso6] without any deuterium labeling in liver samples.</p

Sample time course trajectories of deuterium labeled triacylglycerols detected in liver, eWAT and sWAT samples.

<p>(A) TG(16∶0/18∶2/20∶4)[iso6] with one ²H label and one Na⁺ as adduct ion in liver samples. (B) TG(16∶0/16∶1/16∶1)[iso3] with one ²H label and an adduct ion of Na⁺ eWAT samples. (C) TG(16∶0/16∶0/18∶1)[iso3] with one ²H label and an adduct ion of Na⁺ in sWAT samples.</p