Dataset Information

GNPS - Luxembourgish surface water samples 2019-2022

ABSTRACT: mzML files from the analysis of SPE-concentrated surface water samples collected in different rivers in Luxembourg between 2019 and 2022 through the collaborative work between the Environmental Cheminformatics Group (LCSB, University of Luxembourg) and the Luxembourg Administration de la gestion de l eau (AGE). The according sampling locations related to each file can be found in the supplementary xlsx file.

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): No Species

SUBMITTER: Emma Schymanski

PROVIDER: MSV000092221 | GNPS | Wed Jun 21 01:58:00 BST 2023

REPOSITORIES: GNPS

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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)

Dataset Information

GNPS - Luxembourgish surface water samples 2019-2022

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