Fram Strait and Barents Sea
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB50022 | ENA |
REPOSITORIES: ENA
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Project description:Ocean microbiome dataset published by [May2016] and the corresponding database search results. The LC-MS/MS spectra are from triplicate acquisitions of peptides, acquisitions 51-53 from the Bering Strait (BSt) and acquisitions 45-47 from the Chukchi Sea (CS). For each sampling location, there are two sets of spectrum identifications: one based on a metapeptide database specific to the location (metapeptides_BSt and metapeptides_CS) and one based on a non-redundant environmental database (env_nr). Spectrum identifications were obtained with Tide and Percolator as described in [Yilmaz2023]. Casanovo predictions for this dataset are provided in MSV000093980, alongside Casanovo predictions for other datasets. ________________________________ PUBLICATIONS: [May2016] May, D. H. et al. "An Alignment-Free Metapeptide Strategy for Metaproteomic Characterization of Microbiome Samples Using Shotgun Metagenomic Sequencing." Journal of Proteome Research. 2016. [Yilmaz2023] Yilmaz, Melih et al. "Sequence-to-sequence translation from mass spectra to peptides with a transformer model." Nature Communications. 2024. ________________________________ SPECTRUM FILES: The dataset contains the following six spectrum files, three from the Chukchi Sea (2016_Jan_12_QE2_45.mzXML, 2016_Jan_12_QE2_46.mzXML, 2016_Jan_12_QE2_47.mzXML) and three from the Bering Strait (2016_Jan_12_QE3_51.mzXML, 2016_Jan_12_QE3_52.mzXML, 2016_Jan_12_QE3_53.mzXML). ________________________________ FASTA FILES: The dataset containes three protein fasta files: Bering Strait proteins in metapeptides_BSt.fasta, Chukchi Sea proteins in metapeptides_CS.fasta, and the environmental protein database in env_nr.fasta. ________________________________ SEARCH FILES: Associated with each FASTA file is a tide-index log file with names of the form <database>.tide-index.log.txt. The dataset contains Tide output files for 12 searches (six spectrum files, each searched against two databases). For each search, the corresponding tide-search primary output files have names like <sample>.<database>.tide-search.target.txt. There are also corresponding log files and parameter files with names like <sample>.<database>.tide-search.log.txt and <sample>.<database>.tide-search.params.txt. ________________________________ PERCOLATOR FILES: The dataset contains four sets of Percolator output files. The Percolator PSM-level output files are named <location>.<database>.percolator.target.psms.txt, where <location> is "BSt" for Bering Strait and "CS" for Chukchi Sea, and <database> is "metapeptide_BSt", "metapeptide_CS" or "env_nr". The peptide-level output files are <location>.<database>.percolator.target.peptides.txt. The corresponding log files are <location>.<database>.percolator.log.txt. And the lists of peptides accepted at 1% FDR are <location>.<database>.peptides.q01.txt. ________________________________ CASANOVO FILES: Casanovo peptide predictions for this dataset reside in MSV000093980, and they are organized into six mzTab files where each file is named after the corresponding spectrum file. (e.g. 2016_Jan_12_QE2_45.mztab)
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Project description:We sampled the microbial community at the sea ice edge in McMurdo Sound, Ross Sea at the same location (-77.62S, 165.41E) for four weeks (as described in Wu et al 2019, Nat. Comms.). We had four sampling dates corresponding to weeks 1 to 4: December 28 2014, January 6, 15, and 22 2015. Large volumes of water (150--250 L) were filtered from 1 m depth at the sea ice edge, and passed through three filters sequentially (3.0, 0.8, and 0.1 um, each 293 mm Supor filters). Filters with collected biomass were then placed in tubes with a sucrose-based preservative buffer (20 mM EDTA, 400 mM NaCl, 0.75 M sucrose, 50 mM Tris-HCl, pH 8.0) and stored at -80 C until sample processing. We extracted proteins after buffer exchange into a 3\% SDS solution as previously described Wu et al 2019, Nat. Comms.
2021-09-07 | PXD022995 | Pride
Project description:Ocean microbiome dataset published by May et al. [May2016] and the corresponding peptide identifications. The LC-MS/MS spectra are from triplicate acquisitions of peptides, acquisitions 51-53 from the Bering Strait (BSt) and acquisitions 45-47 from the Chukchi Sea (CS). For each sampling location, there are two sets of peptide identifications: one based on a metapeptide database specific to the location and one based on a non-redundant environmental database. Peptide identifications were obtained with Tide search and Percolator as described in Yilmaz et al. [Yilmaz2023].
[May2016] May, D. H. et al. "An Alignment-Free Metapeptide Strategy for Metaproteomic Characterization of Microbiome Samples Using Shotgun Metagenomic Sequencing", Journal of Proteome Research, 2016.
[Yilmaz2023] Yilmaz, Melih et al. "Sequence-to-sequence translation from mass spectra to peptides with a transformer model", bioRxiv, 2023.
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Project description:Sea cucumbers (Holothuroidea; Echinodermata), cycle annually between aestivation when water temperature is above about 25°C in the summer and active life when temperature is below about 18°C. We used RNA-Seq to determine gene expression profiles of intestine tissue of A.japonicus during non-aestivation (NA), deep-aestivation (DA), and arousal from aestivation (AA). At least 15 individuals per stage, intestines at NA, DA and AA stages were used for our experiments.
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