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1,448 results for “Proteomics”
TPE-MI reveals proteome remodelling in response to pharmacological stimuli
<p>Dataset contains raw and preprocessed data for fluorescence and proteomic studies respectively. In each case, protein foldedness was probed using thiol reactivity. The raw mass spectrometry proteomics data have also been deposited to the ProteomeXchange Consortium via the PRIDE partner repository, with the dataset identifiers PXD033152.</p>
Characterization of the nuclear proteome of Chlamydomonas in response to salt stress
<p><strong>Supplementary Files and Figures for the manuscript </strong></p> <p><strong>"Characterization of the nuclear proteome of Chlamydomonas in response to salt stressCharacterization of the nuclear proteome of Chlamydomonas in response to salt stress"</strong></p>
SETH predictions for Swiss-Prot (downloaded 13/06/22) and the human proteome (downloaded 08/07/21)
<p>Per residue disorder predictions for proteins of Swiss-Prot (downloaded 13/06/22) and the human proteome (downloaded 08/07/21; (The UniProt et al., 2021)) generated with SETH (<a href="https://github.com/DagmarIlz/SETH">https://github.com/DagmarIlz/SETH</a>). </p> <p>For details on SETH see: Ilzhöfer D, Heinzinger M and Rost B (2022) SETH predicts nuances of residue disorder from protein embeddings. Front. Bioinform. 2:1019597. <a href="https://doi.org/10.3389/fbinf.2022.1019597">https://doi.org/10.3389/fbinf.2022.1019597</a>.</p> <p>For some proteins no ProtT5 (Elnaggar et al., 2021) embeddings could be generated due to their length. Therefore, these proteins are missing from the dataset. All in all, predictions for 567,458 out of 567,483 proteins are available for Swiss-Prot and 20,352 proteins are available for the human proteome.</p>
Combined network file for "FAVA: High-quality functional association networks inferred from scRNA-seq and proteomics data"
<p><strong>Combined network from scRNA-seq and proteomics data</strong></p> <p>Given the complementary nature of the networks based on scRNA-seq and proteomics data individually, we decided to combine them into a single network. As the Pearson Correlation Coefficient scores from FAVA cannot be assumed to be directly comparable across the two networks, we converted them to probabilistic scores based on the KEGG benchmarks. These calibrated scores were then combined to produce a single network based on scRNA-seq as well as proteomics data. As should be expected, this network outperforms the individual networks, combining the best aspects of both.</p>
Alternatively_coded_phage_proteomics
<p>Genomes for 2 alternatively coded phages in our proteomics study, and a .tsv with accession numbers for associated datasets. </p>
Proteomic data sets after selecting mitochondrial proteins from the scaffold software for Ingenuity Pathway analysis (IPA Qiagen)
<p>List of fold change proteomic data sets of dFCM- 39 vs. 12Day and105 vs. 12Day, cFCM- 40 vs. 12Day and115 vs. 12Day , mouse heart 90 vs. 1 day after selecting mitochondrial proteins from the scaffold software for Ingenuity Pathway Analysis (IPA Qiagen)</p>
Fig. 6 in Salivary gland proteome analysis of developing adult female HaemaphYSaliS longiCorniS ticks: molecular motor and TCA cycle-related proteins play an important role throughout development
Fig. 6 Phenotype associated with dynein, kinesin, isocitrate dehydrogenase and citrate synthase mRNA subjected to RNAi in female ticks via injection with the corresponding dsRNA. a Dynein dsRNA injection. b Kinesin dsRNA injection. c Isocitrate dehydrogenase dsRNA injection. d Citrate synthase dsRNA injection. e GFP dsRNA injection, control. f No injection, control. Scale-bars: 5 mm
Fig. 7 in Salivary gland proteome analysis of developing adult female HaemaphYSaliS longiCorniS ticks: molecular motor and TCA cycle-related proteins play an important role throughout development
Fig. 7 Digital micrographs of salivary gland acinar morphological changes in unfed female H. longicornis after RNAi.The time at which the tick bit the host and began sucking blood was recorded as day 0. a–e Dynein dsRNA injection. f–j Kinesin dsRNA injection. k–o Isocitrate dehydrogenase dsRNA injection. p–t Citrate synthase dsRNA injection. u–y GFP dsRNA injection, control. Scale-bars: 25 µm
Fig. 4 in Salivary gland proteome analysis of developing adult female HaemaphYSaliS longiCorniS ticks: molecular motor and TCA cycle-related proteins play an important role throughout development
Fig. 4 KEGG pathway enrichment analysis of the differentially expressed proteins in 5 different Clusters. Terms with a P-value <0.05 were used to draw the column diagrams. a–e KEGG pathway enrichment for the proteins in Cluster 1 to Cluster 5
Fig. 3 in Salivary gland proteome analysis of developing adult female HaemaphYSaliS longiCorniS ticks: molecular motor and TCA cycle-related proteins play an important role throughout development
Fig. 3 GO functional annotations for all the differentially expressed proteins. a–c GO annotations of differentially expressed proteins in the salivary glands of partially fed ticks compared with unfed ticks (115:114). d–f GO annotations of differentially expressed proteins in the salivary glands of mated semi-engorged ticks compared with partially fed ticks (116:115). g–i GO annotations of differentially expressed proteins in the salivary glands of engorged ticks compared with mated semi-engorged ticks (117:116). Abbreviations: BP, biological process; CC, cellular component; MF, molecular function; CO, cellular component organization or biogenesis
Fig. 5 in Salivary gland proteome analysis of developing adult female HaemaphYSaliS longiCorniS ticks: molecular motor and TCA cycle-related proteins play an important role throughout development
Fig. 5 RT-qPCR analyzed the mRNA expression levels of dynein, kinesin, isocitrate dehydrogenase, and citrate synthase during the four feeding stages of salivary gland development
Fig. 2 in Salivary gland proteome analysis of developing adult female HaemaphYSaliS longiCorniS ticks: molecular motor and TCA cycle-related proteins play an important role throughout development
Fig. 2 Statistics and cluster analysis for the identified proteins and their expression levels in the salivary glands of female H. longicornis. a Venn diagram showing the number of proteins (with CV <20%) identified in the three experiments. b Venn diagram showing the number of proteins with quantitative information. c Cluster analysis according to trends in protein expression in the salivary glands of female ticks
Fig. 1 in Salivary gland proteome analysis of developing adult female HaemaphYSaliS longiCorniS ticks: molecular motor and TCA cycle-related proteins play an important role throughout development
Fig. 1 Workflow for quantitative proteomics analysis of changes in protein expression in the salivary glands of female H. longicornis during the blood-feeding process
DATASET - Mass Spectrometry - Snake venom proteomics of three subspecies of the North African mountain viper (Vipera monticola, Saint-Girons 1954) from Morocco
<p><strong>This DATASET collection includes the mass spectrometry files for proteomics venom investigation of three subspecies of the North African mountain viper (<em>Vipera monticola</em>, Saint-Girons 1954) from Morocco.</strong></p> <p><strong>Species list:</strong></p> <ol> <li>Vipera monticola monticola</li> <li>Vipera monticola atlantica</li> <li>Vipera monticola saintgironsi</li> </ol> <p><strong>Folders 01-03 - BOTTOM-UP PROTEOMICS</strong>: The venom pools were investigated by the bottom-up "snake venomics" (labled as SVX) approach and in short: separated by RP-HPLC, followed by SDS-PAGE separation and the single bands were in-gel processed by DTT, IAC and finally o/n tryptic digested. Samples submitted to HPLC-MS/MS. Early peptidic fractions of the first HPLC run were directly submitted to HPLC-MS/MS analytic w/o further gel procession. Folders 01 to 03 include the MS and MS/MS spectra of the snake species 1-3, respectively. Files are included as RAW and MZML format.</p> <p>Used instrument: LTQ Orbitrap XL mass spectrometer (Thermo, Bremen, Germany) with an Agilent 1260 HPLC system (Agilent Technologies, Waldbronn, Germany) using a reversed-phase Grace Vydac 218MS C18 (2.1 × 150 mm; 5 μm particle size) column.</p> <p>Modifications: UNIMOD:4 - \"Iodoacetamide derivative.\"</p> <p>Used protein database: Uniprot_8570_serpentes_reviewed_CandIso_2747_entries_230398.fasta</p>
Scripts and analysis files for categorization of PKZILLA matching proteomic peptides into protein-unique, protein-multimatch & exon-unique, exon-multimatch categories.
<p>A .zip file containing the source data files & Jupyter notebook for analysis of the <em>Prymnesium parvum</em> 12B1 PKZILLA-detecting proteomic results (<a href="https://doi.org/10.5281/zenodo.10023441">https://doi.org/10.5281/zenodo.10023441</a>), and the resulting files from the workflow. See "Analysis of proteomic results" section of the manuscript Materials and Methods for further detail. </p> <p><strong>Key files:</strong></p> <ul> <li>'PKZILLA-1_classify_peptides.txt' - A plaintext report of the # of classified peptides for PKZILLA-1</li> <li>'PKZILLA-2_classify_peptides.txt' - A plaintext report of the # of classified peptides for PKZILLA-2</li> <li>'./hierarchical_classified_xlsx/' - Excel spreadsheets with the classified peptides for PKZILLA-1 and PKZILLA-2</li> <li>'./Process_into_polypeptide_coordinates/' - Workflow, results, and plots for back-alignment of peptides back to PKZILLA-1 and PKZILLA-2 genomic loci</li> </ul>
Supplementary Material for "Can ZooMS help assess species abundance in highly fragmented bone assemblages? Integrating morphological and proteomic identifications for the calculation of an adjusted ZooMS-eNISP"
<p><span>Supplementary Material for the article "Can ZooMS help assess species abundance in highly fragmented bone assemblages? Integrating morphological and proteomic identifications for the calculation of an adjusted ZooMS-eNISP" by Discamps et al., published in Palaeoanthropology.</span></p> <p><span>SI#1 Cassenade dataset (morphological and ZooMS identifications, sizes, masses, etc.) in RDS format.</span></p> <p><span>SI#2 Cassenade dataset (morphological and ZooMS identifications, sizes, masses, etc.) in CSV format.</span></p> <p><span>SI#3 R script used for making the figures and statistical tests</span></p>
DATASET - Mass Spectrometry - Snake venom proteomics of island and mainland V. ammodytes populations from North Macedonia
<p><strong><span>This DATASET collection includes the mass spectrometry files for proteomics venom investigation of island and mainland <em>V. ammodytes</em> populations from North Macedonia.</span></strong></p> <p><strong><span>Sample list:</span></strong></p> <ol> <li><span>Island - adult - male</span></li> <li><span>Island - adult - female</span></li> <li><span>Island - juvenile</span></li> <li><span>Island - subadult</span></li> <li><span>Mainland - adult</span></li> <li><span>Mainland - subadult</span></li> <li><span>Mainland - juvenile</span></li> </ol> <p><strong><span>Folders 01-07 - BOTTOM-UP PROTEOMICS</span></strong><span>: The venom pools were investigated by the bottom-up "snake venomics" (labelled as SVX) approach and in short: separated by RP-HPLC, followed by SDS-PAGE separation and the single bands were in-gel processed by DTT, IAC and finally o/n tryptic digested. Samples submitted to HPLC-MS/MS. Early peptidic fractions of the first HPLC run were directly submitted to HPLC-MS/MS analytic w/o further gel procession. Folders 01 to 07 include the MS and MS/MS spectra of the <em>V. ammodytes</em> sample pools from different populations. Files are included as RAW and MZML format.</span></p> <p><span>Used instrument: LTQ Orbitrap XL mass spectrometer (Thermo, Bremen, Germany) with an Agilent 1260 HPLC system (Agilent Technologies, Waldbronn, Germany) using a reversed-phase Grace Vydac 218MS C18 (2.1 × 150 mm; 5 </span><span>μ</span><span>m particle size) column.</span></p> <p><span>Modifications: UNIMOD:4 - \"Iodoacetamide derivative.\"</span></p> <p><span>Used protein database: Uniprot_8750_serpentes_CanNIso_2674_entries_220210_cRAP_220210.fasta</span></p>
Fig. 1. 2D in Proteomic profile of Ortleppascaris sp.: A helminth parasite of Rhinella marina in the Amazonian region
Fig. 1. 2D gel containing the somatic extract of Ortleppascaris sp. larvae. See Table 1 for details.
Fig. 1 in Ortleppascaris sp. and your host Rhinella marina: A proteomic view into a nematode-amphibian relationship
Fig. 1. Two-dimensional gel of proteins originating from cystic fluid of Ortleppascaris sp. encystment.
Yeast proteomics microflow 23 min gradient DIA-MS
<p><em>Saccharomyces cerevisiae</em> (BY4743 rendered prototrophic with a plasmid encoding for HIS3, LEU2 and URA3 <a href="https://paperpile.com/c/AXHME6/nwrF">[25]</a>) were grown to exponential phase in minimal synthetic nutrient media. Proteins were extracted by bead beating for 5min at 1500rpm in 8M urea/0.1M ammonium bicarbonate. Proteins were reduced with 5mM dithiothreitol, alkylated with 10mM iodoacetamide. The sample was diluted to 1.5M urea/0.1M ammonium bicarbonate before the proteins were digested overnight with Trypsin (1:30 Trypsin to total protein ratio). Peptides were cleaned-up with 96-well MacroSpin plates (Nest Group) and iRT peptides (Biognosys AG) were spiked in.</p> <p>The digested peptides were analysed on a nanoAcquity (Waters) coupled to a TripleTOF 6600 (Sciex). Peptides were separated with a 23 minute non-linear gradient (4% Acetonitrile/0.1 % formic acid to 36% Acetonitrile/0.1% formic acid) on a Waters HSS T3 column (150mm x 300μm, 1.8μm Particles) with a 5μl/min flow rate. The DIA method consisted of an MS1 scan from m/z 400 to m/z 1250 (50ms accumulation time) and 40 MS2 scans (35ms accumulation time) with variable precursor isolation width covering the mass range from m/z 400 to m/z 1250.</p>
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
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International Brain Laboratory public data
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OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.