Ontology highlight
ABSTRACT:
PROVIDER: PRJNA765567 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR16019889_1.fastq.gz | Fastqsanger.gz | |||
| SRR16019890_1.fastq.gz | Fastqsanger.gz | |||
| SRR16019891_1.fastq.gz | Fastqsanger.gz | |||
| SRR16019892_1.fastq.gz | Fastqsanger.gz | |||
| SRR16019893_1.fastq.gz | Fastqsanger.gz |
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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.
2024-03-27 | MSV000094415 | MassIVE
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)
2024-05-07 | MSV000094709 | MassIVE
Project description:Analysis of bacterial fraction collected on GF/F filters post pre-filtration on 1um filter. 15L were filtered from Bering Strait (BSt) surface water and Chukchi Sea (station 2) bottom waters.
2019-01-25 | PXD006472 | Pride