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R Code and Images for Developing a Spatial Concordance Coefficient at Harvard Forest 2010
Concordance correlation coefficients have been developed in a variety of different contexts. This problem has been widely addressed in a non-spatial context, but here we consider a coefficient that for a fixed spatial lag allows the comparison of two spatial sequences (e.g., images). We define a spatial concordance coefficient for second-order stationary processes.
Negation and negative concord in AIS and ALF examples
<p>The file contains metadata on 22500 negative sentences from 1046 Italo-, Gallo-, and Rhaeto-Romance dialects. It is based on primary data from the <em>Atlas linguistique de la France</em> (ALF; Gilliéron and Edmont 1902-1910) and the <em>Sprach- und Sachatlas Italiens und der Südschweiz</em> (AIS; Jaberg and Jud 1928-1940).</p> <p>This dataset is a research output of the project <strong>Coding Syntactic Microvariation</strong> (CoSMic), funded by the IDEX programme of the Université Côte d'Azur (CSI Recherche 2021).</p> <p>This file is shared under the Creative Commons Attribution CC BY-NC-SA license.<br> </p>
Concordant inter-laboratory derived concentrations of ceramides in human plasma reference materials via authentic standards
<h1>Concordant inter-laboratory derived concentrations of ceramides in human plasma reference materials via authentic standards</h1> <p>In this community effort, we compared measurements between 34 laboratories from 19 countries, utilizing mixtures of labelled authentic synthetic standards, to quantify by mass spectrometry four clinically used ceramide species in the NIST (National Institute of Standards and Technology) human blood plasma Standard Reference Material (SRM) 1950, as well as new suite of candidate plasma reference materials (RM 8231). Participants either utilized a provided validated method (SOP) and/or their method of choice (OTHER). Mean concentration values, and intra- and inter-laboratory coefficients of variation (CV) were calculated using single-point and multi-point calibrations, respectively.</p> <p>The attached file "ILS-Ceramide-Ring-Trial-Datasets.csv" and the table below map the lab number (LabNum) used in the manuscript in all plots to the originally assigned submission Id (LabId) used in <a href="https://github.com/lifs-tools/ils-ceramide-ring-trial/tree/main/data/original-reports" target="_blank" rel="noopener">the anonymized reports </a>containing the peak areas submitted by each lab for their SOP (Standard) and / or OTHER (Preferred) workflow. The table below provides further information on the separation used (LC), the mass analyzer type (QQQ=Triple Quads and Traps, Orbitrap, TOF) and the associated mass analyzer resolution (LowRes, HighRes), and links each LabNum to the corresponding dataset name and Zenodo DOI, if available. In order to retain the anonymity of all participating labs w.r.t. the submitted datasets, only the converted mzML files are provided in the linked submissions. Please note that labs were free to choose whether they wanted to disclose their MS data or not. Thus, missing datasets indicate that the corresponding lab did not provide their raw / mzML data. </p> <p>All reports together with the code for analysis and visualization, reproducing the figures in the manuscript, are available under the following doi: <a href="../doi/10.5281/zenodo.10081970" target="_blank" rel="noopener">https://zenodo.org/doi/10.5281/zenodo.10081970</a>. This links to releases of the following GitHub repository: <a href="https://github.com/lifs-tools/ils-ceramide-ring-trial">https://github.com/lifs-tools/ils-ceramide-ring-trial</a>. </p> <h2>Ring Trial mzML Datasets</h2> <table> <tbody> <tr> <th>LabNum</th> <th>LabId</th> <th>Protocol</th> <th>LC</th> <th>MassAnalyzerType</th> <th>MassAnalyzerResolution</th> <th>DatasetName</th> <th>DOI</th> </tr> <tr> <td>1</td> <td>02b</td> <td>SOP</td> <td>RP</td> <td>QQQ</td> <td>LowRes</td> <td>Lab_01_SOP</td> <td><a href="https://doi.org/10.5281/zenodo.13134264" target="_blank" rel="noopener">10.5281/zenodo.13134264</a></td> </tr> <tr> <td>2</td> <td>3</td> <td>OTHER</td> <td>RP</td> <td>QQQ</td> <td>LowRes</td> <td>Lab_02_OTHER</td> <td><a href="https://doi.org/10.5281/zenodo.13145059" target="_blank" rel="noopener">10.5281/zenodo.13145059</a></td> </tr> <tr> <td>3</td> <td>4</td> <td>SOP</td> <td>RP</td> <td>QQQ</td> <td>LowRes</td> <td>Lab_03_SOP</td> <td><a href="https://doi.org/10.5281/zenodo.13134437" target="_blank" rel="noopener">10.5281/zenodo.13134437</a></td> </tr> <tr> <td>4</td> <td>5</td> <td>OTHER</td> <td>RP</td> <td>QQQ</td> <td>LowRes</td> <td>Lab_04_OTHER</td> <td> </td> </tr> <tr> <td>5</td> <td>7</td> <td>OTHER</td> <td>RP</td> <td>Orbitrap</td> <td>HighRes</td> <td>Lab_05_OTHER</td> <td><a href="https://doi.org/10.5281/zenodo.13134439" target="_blank" rel="noopener">10.5281/zenodo.13134439</a></td> </tr> <tr> <td>6</td> <td>9</td> <td>OTHER</td> <td>FIA</td> <td>QQQ</td> <td>LowRes</td> <td>Lab_06_OTHER</td> <td><a href="https://doi.org/10.5281/zenodo.13134441" target="_blank" rel="noopener">10.5281/zenodo.13134441</a></td> </tr> <tr> <td>7</td> <td>10a</td> <td>SOP</td> <td>RP</td> <td>QQQ</td> <td>LowRes</td> <td>Lab_07_SOP</td> <td><a href="https://doi.org/10.5281/zenodo.13134445" target="_blank" rel="noopener">10.5281/zenodo.13134445</a></td> </tr> <tr> <td>7</td> <td>10b</td> <td>OTHER</td> <td>RP</td> <td>QQQ</td> <td>LowRes</td> <td>Lab_07_OTHER</td> <td><a href="https://doi.org/10.5281/zenodo.13134443" target="_blank" rel="noopener">10.5281/zenodo.13134443</a></td> </tr> <tr> <td>8</td> <td>12</td> <td>SOP</td> <td>RP</td> <td>QQQ</td> <td>LowRes</td> <td>Lab_08_SOP</td> <td><a href="https://doi.org/10.5281/zenodo.13134447" target="_blank" rel="noopener">10.5281/zenodo.13134447</a></td> </tr> <tr> <td>9</td> <td>13</td> <td>OTHER</td> <td>RP</td> <td>QQQ</td> <td>LowRes</td> <td>Lab_09_OTHER</td> <td> </td> </tr> <tr> <td>10</td> <td>14</td> <td>SOP</td> <td>RP</td> <td>QQQ</td> <td>LowRes</td> <td>Lab_10_SOP</td> <td> </td> </tr> <tr> <td>11</td> <td>15</td> <td>SOP</td> <td>RP</td> <td>QQQ</td> <td>LowRes</td> <td>Lab_11_SOP</td> <td><a href="https://doi.org/10.5281/zenodo.13134449" target="_blank" rel="noopener">10.5281/zenodo.13134449</a></td> </tr> <tr> <td>12</td> <td>16</td> <td>OTHER</td> <td>RP</td> <td>Orbitrap</td> <td>HighRes</td> <td>Lab_12_OTHER</td> <td><a href="https://doi.org/10.5281/zenodo.13134451" target="_blank" rel="noopener">10.5281/zenodo.13134451</a></td> </tr> <tr> <td>13</td> <td>17a</td> <td>OTHER</td> <td>RP</td> <td>TOF</td> <td>HighRes</td> <td>Lab_13_OTHER</td> <td> </td> </tr> <tr> <td>14</td> <td>18a</td> <td>SOP</td> <td>RP</td> <td>QQQ</td> <td>LowRes</td> <td>Lab_14_SOP</td> <td><a href="https://doi.org/10.5281/zenodo.13135617" target="_blank" rel="noopener">10.5281/zenodo.13135617</a></td> </tr> <tr> <td>14</td> <td>18b</td> <td>SOP</td> <td>RP</td> <td>QQQ</td> <td>LowRes</td> <td>Lab_14_SOP</td> <td><a href="https://doi.org/10.5281/zenodo.13135617" target="_blank" rel="noopener">10.5281/zenodo.13135617</a></td> </tr> <tr> <td>15</td> <td>19</td> <td>SOP</td> <td>RP</td> <td>QQQ</td> <td>LowRes</td> <td>Lab_15_SOP</td> <td><a href="https://doi.org/10.5281/zenodo.13135625" target="_blank" rel="noopener">10.5281/zenodo.13135625</a></td> </tr> <tr> <td>16</td> <td>20a</td> <td>SOP</td> <td>RP</td> <td>QQQ</td> <td>LowRes</td> <td>Lab_16_SOP</td> <td> </td> </tr> <tr> <td>16</td> <td>20b</td> <td>OTHER</td> <td>RP</td> <td>QQQ</td> <td>LowRes</td> <td>Lab_16_OTHER</td> <td> </td> </tr> <tr> <td>17</td> <td>21</td> <td>SOP</td> <td>RP</td> <td>QQQ</td> <td>LowRes</td> <td>Lab_17_SOP</td> <td> </td> </tr> <tr> <td>18</td> <td>22</td> <td>SOP</td> <td>RP</td> <td>QQQ</td> <td>LowRes</td> <td>Lab_18_SOP</td> <td><a href="https://doi.org/10.5281/zenodo.13135627" target="_blank" rel="noopener">10.5281/zenodo.13135627</a></td> </tr> <tr> <td>19</td> <td>23</td> <td>SOP</td> <td>RP</td> <td>QQQ</td> <td>LowRes</td> <td>Lab_19_SOP</td> <td><a href="https://doi.org/10.5281/zenodo.13135629" target="_blank" rel="noopener">10.5281/zenodo.13135629</a></td> </tr> <tr> <td>20</td> <td>24</td> <td>SOP</td> <td>RP</td> <td>QQQ</td> <td>LowRes</td> <td>Lab_20_SOP</td> <td> </td> </tr> <tr> <td>21</td> <td>25</td> <td>SOP</td> <td>RP</td> <td>QQQ</td> <td>LowRes</td> <td>Lab_21_SOP</td> <td><a href="../doi/10.5281/zenodo.13244007" target="_blank" rel="noopener">10.5281/zenodo.13244007</a></td> </tr> <tr> <td>22</td> <td>26a</td> <td>OTHER</td> <td>FIA</td> <td>Orbitrap</td> <td>HighRes</td> <td>Lab_22_OTHER</td> <td> </td> </tr> <tr> <td>22</td> <td>26b</td> <td>OTHER</td> <td>FIA</td> <td>QQQ</td> <td>LowRes</td> <td>Lab_22_OTHER</td> <td> </td> </tr> <tr> <td>23</td> <td>27</td> <td>SOP</td> <td>RP</td> <td>QQQ</td> <td>LowRes</td> <td>Lab_23_SOP</td> <td><a href="https://doi.org/10.5281/zenodo.13135632" target="_blank" rel="noopener">10.5281/zenodo.13135632</a></td> </tr> <tr> <td>24</td> <td>28</td> <td>SOP</td> <td>RP</td> <td>QQQ</td> <td>LowRes</td> <td>Lab_24_SOP</td> <td><a href="https://doi.org/10.5281/zenodo.13135634" target="_blank" rel="noopener">10.5281/zenodo.13135634</a></td> </tr> <tr> <td>25</td> <td>29a</td> <td>SOP</td> <td>RP</td> <td>TOF</td> <td>HighRes</td> <td>Lab_25_SOP</td> <td><a href="https://doi.org/10.5281/zenodo.13136167" target="_blank" rel="noopener">10.5281/zenodo.13136167</a></td> </tr> <tr> <td>25</td> <td>29b</td> <td>OTHER</td> <td>SFC</td> <td>QQQ</td> <td>LowRes</td> <td>Lab_25_OTHER</td> <td><a href="https://doi.org/10.5281/zenodo.13135638" target="_blank" rel="noopener">10.5281/zenodo.13135638</a></td> </tr> <tr> <td>26</td> <td>30</td> <td>SOP</td> <td>RP</td> <td>QQQ</td> <td>LowRes</td> <td>Lab_26_SOP</td> <td><a href="https://doi.org/10.5281/zenodo.13136171" target="_blank" rel="noopener">10.5281/zenodo.13136171</a></td> </tr> <tr> <td>27</td> <td>31</td> <td>SOP</td> <td>RP</td> <td>QQQ</td> <td>LowRes</td> <td>Lab_27_SOP</td> <td><a href="https://doi.org/10.5281/zenodo.13136176" target="_blank" rel="noopener">10.5281/zenodo.13136176</a></td> </tr> <tr> <td>28</td> <td>32</td> <td>OTHER</td> <td>RP</td> <td>TOF</td> <td>HighRes</td> <td>Lab_28_OTHER</td> <td> </td> </tr> <tr> <td>29</td> <td>33</td> <td>OTHER</td> <td>RP</td> <td>QQQ</td> <td>LowRes</td> <td>Lab_29_OTHER</td> <td> </td> </tr> <tr> <td>30</td> <td>34</td> <td>SOP</td> <td>RP</td> <td>QQQ</td> <td>LowRes</td> <td>Lab_30_SOP</td> <td> </td> </tr> <tr> <td>31</td> <td>35</td> <td>OTHER</td> <td>RP</td> <td>QQQ</td> <td>LowRes</td> <td>Lab_31_OTHER</td> <td> </td> </tr> <tr> <td>32</td> <td>36</td> <td>SOP</td> <td>RP</td> <td>QQQ</td> <td>LowRes</td> <td>Lab_32_SOP</td> <td><a href="../doi/10.5281/zenodo.13166454" target="_blank" rel="noopener">10.5281/zenodo.13166454</a></td> </tr> <tr> <td>33</td> <td>37</td> <td>OTHER</td> <td>RP</td> <td>QQQ</td> <td>LowRes</td> <td>Lab_33_OTHER</td> <td><a href="../doi/10.5281/zenodo.13732469" target="_blank" rel="noopener">10.5281/zenodo.13732469</a></td> </tr> <tr> <td>34</td> <td>38</td> <td>SOP</td> <td>RP</td> <td>QQQ</td> <td>LowRes</td> <td>Lab_34_SOP</td> <td><a href="../doi/10.5281/zenodo.13324807" target="_blank" rel="noopener">10.5281/zenodo.13324807</a></td> </tr> </tbody> </table>
Table S1. Geographical localization of Pinus pseudostrobus Lindley. specimens used in the study and concordance of morphological identification with real-time PCR-HRM assay for Pinus pseudostrobus varieties pseudostrobus, apulcensis, oaxacana and coatepecensis, based on the cluster pattern.
<p>File encloses geographical location of collected Pinus pseudostrobus samples in México, as well as haplotype grouping obtaines from HRM analysis</p>
Concordance and discordance in the phylogenomics of the wrasses and parrotfishes (Teleostei: Labridae)
<p>Phylogenomic analysis of large genome-wide sequence data sets can resolve phylogenetic tree topologies for large species groups, help test the accuracy of and improve resolution for earlier multilocus studies, and reveal the level of agreement or concordance within partitions of the genome for various tree topologies. Here we used a target-capture approach to sequence more than 1,000 single-copy exons for more than 200 labrid fishes together with more than 100 outgroup taxa to generate a new data-rich phylogeny for the family Labridae. Our time-calibrated phylogenetic analysis of exon-capture data pushes the root node age of the family Labridae back into the Cretaceous to about 79 Ma years ago. The monotypic Centrogenys vaigiensis, and the order Uranoscopiformes (stargazers) are identified as the sister lineages of Labridae. The phylogenetic relationships among major labrid subfamilies and within these clades was largely congruent with prior analyses of select mitochondrial and nuclear datasets. However, the position of the tribe Cirrhilabrini (fairy and flame wrasses) showed discordance, resolving either as the sister to a crown julidine clade or alternatively sister to a group formed by the labrines, cheilines and scarines. Exploration of this pattern using multiple approaches leads to slightly higher support for this latter hypothesis, highlighting the importance of genome-level data sets for resolving short internodes at key phylogenetic positions in large, economically important groups of coral reef fishes.</p>
Meta-analysis of diurnal transcriptomics reveals strong patterns of concordance and discordance in mouse liver: processed data
<p>The accumulation of public transcriptomic timeseries data enables robust meta-analyses that were not possible until recently. To assess the consistency of biological rhythms across studies, 43 public mouse liver tissue timeseries totaling 805 RNA-seq samples were obtained and analyzed. Only the control groups of each study were included, to create comparable data. Technical factors in RNA-seq library preparation were the largest contributors to transcriptome-level differences, beyond biological or experiment-specific factors such as lighting conditions. Core clock genes were remarkably consistent in phase across all studies, while phase distributions of other periodic genes were generally less consistent. Overlap of genes identified as rhythmic across studies was generally low, with around 50% between some of the highest sample count studies. Distributions of phases of significant genes were remarkably inconsistent across studies, but genes consistently identified as rhythmic clustered near ZT0 and ZT12 in acrophase. Data was integrated across studies in a JIVE analysis, which showed that the top two components of joint within-study variation are determined by time of day. A shape-invariant model with random effects was fit to the genes to identify the underlying shape of the rhythms, consistent across all studies. This revealed the extent of asymmetric and multimodal genes.<br> <br> This supplemental file provides preprocessed RNA-seq quantifications of all reviewed datasets, as well as results of multiple analyses.</p>
Data for: Effects of testosterone on gene expression are concordant between sexes but divergent across species of Sceloporus lizards
<p>Hormones mediate sexual dimorphism by regulating sex-specific patterns of gene expression, but it is unclear how much of this regulation involves sex-specific hormone levels versus sex-specific transcriptomic responses to the same hormonal signal. Moreover, transcriptomic responses to hormones can evolve, but the extent to which hormonal pleiotropy in gene regulation is conserved across closely related species is not well understood. We addressed these issues by elevating testosterone levels in juvenile females and males of three <em>Sceloporus </em>lizard species prior to sexual divergence in circulating testosterone<em>, </em>then characterizing transcriptomic responses in the liver. In each species, more genes were responsive to testosterone in males than in females, suggesting that early developmental processes prime sex-specific transcriptomic responses to testosterone later in life. However, overall transcriptomic responses to testosterone were concordant between sexes, with no genes exhibiting sex-by-treatment interactions. By contrast, hundreds of genes exhibited species-by-treatment interactions, particularly when comparing distantly related species with different patterns of sexual dimorphism, suggesting evolutionary lability in gene regulation by testosterone. Collectively, our results indicate that early organizational effects may lead to sex-specific differences in the magnitude, but not the direction, of transcriptomic responses to testosterone, and that the hormone-genome interface accrues regulatory changes over evolutionary time.</p>
Fig. 6 in Evolution and systematics of Green Bush-crickets (Orthoptera: Tettigoniidae: Tettigonia) in the Western Palaearctic: testing concordance between molecular, acoustic, and morphological data
Fig. 6 Comparison of the duty cycle in the songs of the T. armeniaca complex and T. caudata (left panel) and the Tettigonia viridissima group (right panel)
Fig. 2 in Evolution and systematics of Green Bush-crickets (Orthoptera: Tettigoniidae: Tettigonia) in the Western Palaearctic: testing concordance between molecular, acoustic, and morphological data
Fig. 2 Oscillograms of the song of the Tettigonia viridissima group (1–9) and T. cantans (10) recorded at two speeds: 1 T. cf. longealata (MO: Ajabo, T = 20 °C), 2 T. cf. vaucheriana (MO: N Fes, T = 20 °C), 3 T. cf. vaucheriana (MO: Bouchfaa W of Taza, T = 21 °C), 4 T. cf. vaucheriana (MO: Tilougguite Pass, T = 23 °C), 5 T. cf. vaucheriana and cf. longealata (MO: El Kebab, T = 25 °C), 6 T. cf. vaucheriana (MO: El Kebab, T = 28–30 °C), 7 T. cf. viridissima (MO: S Aïn Zora, T = 22 °C), 8 T. cf. viridissima (MO: S Aïn Zora, T = 25 °C), 9 T. viridissima (BG: Sofia, T = 27 °C), and 10 T. cantans (IT: Val Malene; from Massa et al. 2012, T = 15 °C)). Scale bar for A is 10 s and for B 2 s
Fig. 5 in Evolution and systematics of Green Bush-crickets (Orthoptera: Tettigoniidae: Tettigonia) in the Western Palaearctic: testing concordance between molecular, acoustic, and morphological data
Fig. 5 Appearance of some taxa of Western Palaearctic Tettigonia (relative size proportions between photos not retained). a T. cantans, male, Germany, Gunzenhausen; b T. cantans, female, Germany, Gunzenhausen; c T. uvarovi Ebner, 1946—male, holotype, Siberia (NHMW), lateral view; d same, dorsal view; e T. caudata, male, Bulgaria, Russe district, Byala; f T. acutipennis Ebner, 1946—male, holotype, "Kleinasien 1914 | Marasch, Tölg. | coll. R. Ebner" (NHMW), dorsal view; g same, lateral view; h T. armeniaca, male, Armenia, Djermuk; i T. armeniaca, male, Turkey, Ispir; j T. viridissima morphotype of longealata, male, Morocco, El Kebab; k T. viridissima morphotype of longealata, female, Morocco, El Kebab; l T. viridissima morphotype of vaucheriana, male, Morocco, El Kebab; and m T. viridissima, male and female in copula, Bulgaria, Haskovo district, Kostilkovo village
Fig. 4 in Evolution and systematics of Green Bush-crickets (Orthoptera: Tettigoniidae: Tettigonia) in the Western Palaearctic: testing concordance between molecular, acoustic, and morphological data
Fig. 4 Phylogenetic tree of the genus Tettigonia based on BI analysis of concatenated COI-ITS1-ITS2 sequences. BI posterior probability (PP) values are shown near resolved branches (only support values above 0.50). Species groups, as defined by genetic and morpho-acoustic data, are distinctly shaded, and the respective branches are marked with an open circle and a capital letter as follows: "A"—T. viridissima group, "B"—T. caudata group, and "C"—T. cantans group. Haplotype codes correspond to Table 1 in the Supplement, followed by morphological identification. Squares on the right side of names correspond to relative wing length: filled squares short wings and open squares long wings;
Fig. 7 in Evolution and systematics of Green Bush-crickets (Orthoptera: Tettigoniidae: Tettigonia) in the Western Palaearctic: testing concordance between molecular, acoustic, and morphological data
Fig. 7 Relationship between the duration of chirps and inter-chirp intervals in T. caudata and the Tettigonia armeniaca complex. Green triangles mark recordings from Ispir, Turkey, where monosyllabic, disyllabic, and polysyllabic songs of T. armeniaca were recorded, as well as a song of T. caudata (Color figure online)
Lab_28_SOP - Concordant inter-laboratory derived concentrations of ceramides in human plasma reference materials via authentic standards
<h1>Lab_28_SOP - Concordant inter-laboratory derived concentrations of ceramides in human plasma reference materials via authentic standards - mzML files</h1><p>This dataset is part of the <a href="https://doi.org/10.5281/zenodo.12632989" target="_blank">ILS Ceramide Ring Trial</a>. The suffix 'SOP' indicates that the results were obtained using the recommended and standard operating procedure protocol to prepare and measure all samples, while the suffix 'OTHER' indicates that the corresponding lab prepared and measured the samples according to their own internal protocol. Please check the corresponding mapping file 'ILS-Ceramide-Ring-Trial-Datasets.csv' in the ILS Ceramide Ring Trial record for a mapping of the originally submitted lab reports and the final lab number as reported in the manuscript.</p><p>All reports together with the code for analysis and visualization, reproducing the figures in the manuscript, are available under the following doi: <a href="https://zenodo.org/doi/10.5281/zenodo.10081970" target="_blank">https://zenodo.org/doi/10.5281/zenodo.10081970</a>. This links to releases of the following GitHub repository: <a href="https://github.com/lifs-tools/ils-ceramide-ring-trial" target="_blank">https://github.com/lifs-tools/ils-ceramide-ring-trial</a>. The archived version of the lab reports, workflow source code and manuscript visualizations are also available <a href="https://zenodo.org/doi/10.5281/zenodo.10081970" target="_blank">here</a>.</p><p>Please note that most datasets have been acquired in MRM mode, such that the msconvert conversion to mzML has stored the MRM data in the chromatogram part of the mzML files.</p> <p>The msconvert Docker container (Proteowizard release: 3.0.24172 (63d00b1), build date Jun 202 2024 20:01:14) was used with the native vendor libraries / peak picking for conversion, using default arguments. m/z values were encoded with 64 bit (default), while intensity values were encoded with 32 bit (default). All binary data was zlib-compressed.</p>
Lab_27_SOP - Concordant inter-laboratory derived concentrations of ceramides in human plasma reference materials via authentic standards
<h1>Lab_27_SOP - Concordant inter-laboratory derived concentrations of ceramides in human plasma reference materials via authentic standards - mzML files</h1><p>This dataset is part of the <a href="https://doi.org/10.5281/zenodo.12632989" target="_blank">ILS Ceramide Ring Trial</a>. The suffix 'SOP' indicates that the results were obtained using the recommended and standard operating procedure protocol to prepare and measure all samples, while the suffix 'OTHER' indicates that the corresponding lab prepared and measured the samples according to their own internal protocol. Please check the corresponding mapping file 'ILS-Ceramide-Ring-Trial-Datasets.csv' in the ILS Ceramide Ring Trial record for a mapping of the originally submitted lab reports and the final lab number as reported in the manuscript.</p><p>All reports together with the code for analysis and visualization, reproducing the figures in the manuscript, are available under the following doi: <a href="https://zenodo.org/doi/10.5281/zenodo.10081970" target="_blank">https://zenodo.org/doi/10.5281/zenodo.10081970</a>. This links to releases of the following GitHub repository: <a href="https://github.com/lifs-tools/ils-ceramide-ring-trial" target="_blank">https://github.com/lifs-tools/ils-ceramide-ring-trial</a>. The archived version of the lab reports, workflow source code and manuscript visualizations are also available <a href="https://zenodo.org/doi/10.5281/zenodo.10081970" target="_blank">here</a>.</p><p>Please note that most datasets have been acquired in MRM mode, such that the msconvert conversion to mzML has stored the MRM data in the chromatogram part of the mzML files.</p> <p>The msconvert Docker container (Proteowizard release: 3.0.24172 (63d00b1), build date Jun 202 2024 20:01:14) was used with the native vendor libraries / peak picking for conversion, using default arguments. m/z values were encoded with 64 bit (default), while intensity values were encoded with 32 bit (default). All binary data was zlib-compressed.</p>
Lab_25_OTHER - Concordant inter-laboratory derived concentrations of ceramides in human plasma reference materials via authentic standards
<h1>Lab_25_OTHER - Concordant inter-laboratory derived concentrations of ceramides in human plasma reference materials via authentic standards - mzML files</h1><p>This dataset is part of the <a href="https://doi.org/10.5281/zenodo.12632989" target="_blank">ILS Ceramide Ring Trial</a>. The suffix 'SOP' indicates that the results were obtained using the recommended and standard operating procedure protocol to prepare and measure all samples, while the suffix 'OTHER' indicates that the corresponding lab prepared and measured the samples according to their own internal protocol. Please check the corresponding mapping file 'ILS-Ceramide-Ring-Trial-Datasets.csv' in the ILS Ceramide Ring Trial record for a mapping of the originally submitted lab reports and the final lab number as reported in the manuscript.</p><p>All reports together with the code for analysis and visualization, reproducing the figures in the manuscript, are available under the following doi: <a href="https://zenodo.org/doi/10.5281/zenodo.10081970" target="_blank">https://zenodo.org/doi/10.5281/zenodo.10081970</a>. This links to releases of the following GitHub repository: <a href="https://github.com/lifs-tools/ils-ceramide-ring-trial" target="_blank">https://github.com/lifs-tools/ils-ceramide-ring-trial</a>. The archived version of the lab reports, workflow source code and manuscript visualizations are also available <a href="https://zenodo.org/doi/10.5281/zenodo.10081970" target="_blank">here</a>.</p><p>Please note that most datasets have been acquired in MRM mode, such that the msconvert conversion to mzML has stored the MRM data in the chromatogram part of the mzML files.</p> <p>The msconvert Docker container (Proteowizard release: 3.0.24172 (63d00b1), build date Jun 202 2024 20:01:14) was used with the native vendor libraries / peak picking for conversion, using default arguments. m/z values were encoded with 64 bit (default), while intensity values were encoded with 32 bit (default). All binary data was zlib-compressed.</p>
Lab_23_SOP - Concordant inter-laboratory derived concentrations of ceramides in human plasma reference materials via authentic standards
<h1>Lab_23_SOP - Concordant inter-laboratory derived concentrations of ceramides in human plasma reference materials via authentic standards - mzML files</h1><p>This dataset is part of the <a href="https://doi.org/10.5281/zenodo.12632989" target="_blank">ILS Ceramide Ring Trial</a>. The suffix 'SOP' indicates that the results were obtained using the recommended and standard operating procedure protocol to prepare and measure all samples, while the suffix 'OTHER' indicates that the corresponding lab prepared and measured the samples according to their own internal protocol. Please check the corresponding mapping file 'ILS-Ceramide-Ring-Trial-Datasets.csv' in the ILS Ceramide Ring Trial record for a mapping of the originally submitted lab reports and the final lab number as reported in the manuscript.</p><p>All reports together with the code for analysis and visualization, reproducing the figures in the manuscript, are available under the following doi: <a href="https://zenodo.org/doi/10.5281/zenodo.10081970" target="_blank">https://zenodo.org/doi/10.5281/zenodo.10081970</a>. This links to releases of the following GitHub repository: <a href="https://github.com/lifs-tools/ils-ceramide-ring-trial" target="_blank">https://github.com/lifs-tools/ils-ceramide-ring-trial</a>. The archived version of the lab reports, workflow source code and manuscript visualizations are also available <a href="https://zenodo.org/doi/10.5281/zenodo.10081970" target="_blank">here</a>.</p><p>Please note that most datasets have been acquired in MRM mode, such that the msconvert conversion to mzML has stored the MRM data in the chromatogram part of the mzML files.</p> <p>The msconvert Docker container (Proteowizard release: 3.0.24172 (63d00b1), build date Jun 202 2024 20:01:14) was used with the native vendor libraries / peak picking for conversion, using default arguments. m/z values were encoded with 64 bit (default), while intensity values were encoded with 32 bit (default). All binary data was zlib-compressed.</p>
Lab_19_SOP - Concordant inter-laboratory derived concentrations of ceramides in human plasma reference materials via authentic standards
<h1>Lab_19_SOP - Concordant inter-laboratory derived concentrations of ceramides in human plasma reference materials via authentic standards - mzML files</h1><p>This dataset is part of the <a href="https://doi.org/10.5281/zenodo.12632989" target="_blank">ILS Ceramide Ring Trial</a>. The suffix 'SOP' indicates that the results were obtained using the recommended and standard operating procedure protocol to prepare and measure all samples, while the suffix 'OTHER' indicates that the corresponding lab prepared and measured the samples according to their own internal protocol. Please check the corresponding mapping file 'ILS-Ceramide-Ring-Trial-Datasets.csv' in the ILS Ceramide Ring Trial record for a mapping of the originally submitted lab reports and the final lab number as reported in the manuscript.</p><p>All reports together with the code for analysis and visualization, reproducing the figures in the manuscript, are available under the following doi: <a href="https://zenodo.org/doi/10.5281/zenodo.10081970" target="_blank">https://zenodo.org/doi/10.5281/zenodo.10081970</a>. This links to releases of the following GitHub repository: <a href="https://github.com/lifs-tools/ils-ceramide-ring-trial" target="_blank">https://github.com/lifs-tools/ils-ceramide-ring-trial</a>. The archived version of the lab reports, workflow source code and manuscript visualizations are also available <a href="https://zenodo.org/doi/10.5281/zenodo.10081970" target="_blank">here</a>.</p><p>Please note that most datasets have been acquired in MRM mode, such that the msconvert conversion to mzML has stored the MRM data in the chromatogram part of the mzML files.</p> <p>The msconvert Docker container (Proteowizard release: 3.0.24172 (63d00b1), build date Jun 202 2024 20:01:14) was used with the native vendor libraries / peak picking for conversion, using default arguments. m/z values were encoded with 64 bit (default), while intensity values were encoded with 32 bit (default). All binary data was zlib-compressed.</p>
Lab_18_SOP - Concordant inter-laboratory derived concentrations of ceramides in human plasma reference materials via authentic standards
<h1>Lab_18_SOP - Concordant inter-laboratory derived concentrations of ceramides in human plasma reference materials via authentic standards - mzML files</h1><p>This dataset is part of the <a href="https://doi.org/10.5281/zenodo.12632989" target="_blank">ILS Ceramide Ring Trial</a>. The suffix 'SOP' indicates that the results were obtained using the recommended and standard operating procedure protocol to prepare and measure all samples, while the suffix 'OTHER' indicates that the corresponding lab prepared and measured the samples according to their own internal protocol. Please check the corresponding mapping file 'ILS-Ceramide-Ring-Trial-Datasets.csv' in the ILS Ceramide Ring Trial record for a mapping of the originally submitted lab reports and the final lab number as reported in the manuscript.</p><p>All reports together with the code for analysis and visualization, reproducing the figures in the manuscript, are available under the following doi: <a href="https://zenodo.org/doi/10.5281/zenodo.10081970" target="_blank">https://zenodo.org/doi/10.5281/zenodo.10081970</a>. This links to releases of the following GitHub repository: <a href="https://github.com/lifs-tools/ils-ceramide-ring-trial" target="_blank">https://github.com/lifs-tools/ils-ceramide-ring-trial</a>. The archived version of the lab reports, workflow source code and manuscript visualizations are also available <a href="https://zenodo.org/doi/10.5281/zenodo.10081970" target="_blank">here</a>.</p><p>Please note that most datasets have been acquired in MRM mode, such that the msconvert conversion to mzML has stored the MRM data in the chromatogram part of the mzML files.</p> <p>The msconvert Docker container (Proteowizard release: 3.0.24172 (63d00b1), build date Jun 202 2024 20:01:14) was used with the native vendor libraries / peak picking for conversion, using default arguments. m/z values were encoded with 64 bit (default), while intensity values were encoded with 32 bit (default). All binary data was zlib-compressed.</p>
Lab_24_SOP - Concordant inter-laboratory derived concentrations of ceramides in human plasma reference materials via authentic standards
<h1>Lab_24_SOP - Concordant inter-laboratory derived concentrations of ceramides in human plasma reference materials via authentic standards - mzML files</h1><p>This dataset is part of the <a href="https://doi.org/10.5281/zenodo.12632989" target="_blank">ILS Ceramide Ring Trial</a>. The suffix 'SOP' indicates that the results were obtained using the recommended and standard operating procedure protocol to prepare and measure all samples, while the suffix 'OTHER' indicates that the corresponding lab prepared and measured the samples according to their own internal protocol. Please check the corresponding mapping file 'ILS-Ceramide-Ring-Trial-Datasets.csv' in the ILS Ceramide Ring Trial record for a mapping of the originally submitted lab reports and the final lab number as reported in the manuscript.</p><p>All reports together with the code for analysis and visualization, reproducing the figures in the manuscript, are available under the following doi: <a href="https://zenodo.org/doi/10.5281/zenodo.10081970" target="_blank">https://zenodo.org/doi/10.5281/zenodo.10081970</a>. This links to releases of the following GitHub repository: <a href="https://github.com/lifs-tools/ils-ceramide-ring-trial" target="_blank">https://github.com/lifs-tools/ils-ceramide-ring-trial</a>. The archived version of the lab reports, workflow source code and manuscript visualizations are also available <a href="https://zenodo.org/doi/10.5281/zenodo.10081970" target="_blank">here</a>.</p><p>Please note that most datasets have been acquired in MRM mode, such that the msconvert conversion to mzML has stored the MRM data in the chromatogram part of the mzML files.</p> <p>The msconvert Docker container (Proteowizard release: 3.0.24172 (63d00b1), build date Jun 202 2024 20:01:14) was used with the native vendor libraries / peak picking for conversion, using default arguments. m/z values were encoded with 64 bit (default), while intensity values were encoded with 32 bit (default). All binary data was zlib-compressed.</p>
Lab_14_SOP - Concordant inter-laboratory derived concentrations of ceramides in human plasma reference materials via authentic standards
<h1>Lab_14_SOP - Concordant inter-laboratory derived concentrations of ceramides in human plasma reference materials via authentic standards - mzML files</h1><p>This dataset is part of the <a href="https://doi.org/10.5281/zenodo.12632989" target="_blank">ILS Ceramide Ring Trial</a>. The suffix 'SOP' indicates that the results were obtained using the recommended and standard operating procedure protocol to prepare and measure all samples, while the suffix 'OTHER' indicates that the corresponding lab prepared and measured the samples according to their own internal protocol. Please check the corresponding mapping file 'ILS-Ceramide-Ring-Trial-Datasets.csv' in the ILS Ceramide Ring Trial record for a mapping of the originally submitted lab reports and the final lab number as reported in the manuscript.</p><p>All reports together with the code for analysis and visualization, reproducing the figures in the manuscript, are available under the following doi: <a href="https://zenodo.org/doi/10.5281/zenodo.10081970" target="_blank">https://zenodo.org/doi/10.5281/zenodo.10081970</a>. This links to releases of the following GitHub repository: <a href="https://github.com/lifs-tools/ils-ceramide-ring-trial" target="_blank">https://github.com/lifs-tools/ils-ceramide-ring-trial</a>. The archived version of the lab reports, workflow source code and manuscript visualizations are also available <a href="https://zenodo.org/doi/10.5281/zenodo.10081970" target="_blank">here</a>.</p><p>Please note that most datasets have been acquired in MRM mode, such that the msconvert conversion to mzML has stored the MRM data in the chromatogram part of the mzML files.</p> <p>The msconvert Docker container (Proteowizard release: 3.0.24172 (63d00b1), build date Jun 202 2024 20:01:14) was used with the native vendor libraries / peak picking for conversion, using default arguments. m/z values were encoded with 64 bit (default), while intensity values were encoded with 32 bit (default). All binary data was zlib-compressed.</p>
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