Dataset Information

GNPS Genomics Demo Submission

ABSTRACT: This is a demo GNPS-genomics submission, providing an example of a submission that is compatible with NRPquest / RiPPquest / Glycogenomics and other MS/MS-genomic tools that are becoming available at GNPS. MS/MS data should be uploaded as Peak List / Raw Spectrum as usual. Sequence data should be uploaded as "Sequence Databases" in fasta format. In addition, the user need to create an excel file described below, save it as "Tab Delimited Text (.txt)" with the name "metabolome_genome_link.txt", and upload it as "Supplementary Files". metabolome_genome_link.txt file should have a first row header "SpectrumFile SequenceFile" and then in each row, there should be a spectrum file and a sequence file that the spectrum file should be searched against. An example can be : SpectrumFile SequenceFile spectrum_1.mzXML sequence_1.fasta spectrum_2a.mzXML sequence_2.fasta spectrum_2b.mzXML sequence_2.fasta spectrum_3.mzXML sequence_3a.fasta spectrum_3.mzXML sequence_3b.fasta In this case, spectrum_1.mzXML gets searched against seqeunce_1.mzXML, spectrum_2a.mzXML and spectrum_2b.mzXML get searched against sequence_2.fasta, and spectrum_3.mzXML gets searched against both sequence_3a.fasta and sequence_3b.fasta. To avoid time-consuming sequence data uploads, the user also have the option to simply put refseq or genbank accession numbers instead of uploading a fasta file as "Sequence database". To do this, the user should enter "#RefSeq:" and "#GeneBank:" followed by RefSeq or GeneBank accession. For example both spectrum_albus.mzXML #RefSeq:GCF_000359525.1 and spectrum_albus.mzXML #GenBank:GCA_000359525.1 are valid entries, and they search spectrum_albus.mzXML against : http://www.ncbi.nlm.nih.gov/assembly/GCF_000359525.1/ Please see the demo dataset submission for more information.

INSTRUMENT(S): LTQ Orbitrap Velos

ORGANISM(S): Streptomyces

SUBMITTER: Pavel Pevzner

PROVIDER: MSV000079531 | GNPS | Thu Feb 25 17:18:00 GMT 2016

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 Genomics Demo Submission

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