The Ocean Archive System searches our original datasets as they were submitted to us, not individual points or profiles. If you want to search and retrieve ocean profiles in a common format, or objectively analyzed fields, your better option may be to use one of our project applications. See: Access Data
OAS accession Detail for 0277922
| << previous | |revision: 1 |
| accessions_id: | 0277922 | archive |
|---|---|
| Title: | Nitrite Oxidoreductase targeted metaproteomics from R/V Kilo Moana cruise KM1128 and R/V Falkor cruise FK160115 in the Central Pacific Ocean in 2011 and 2016 (NCEI Accession 0277922) |
| Abstract: | This dataset contains chemical and physical data collected on R/V Falkor and R/V Kilo Moana during cruises FK160115 and KM1128 from 2011-10-05 to 2016-01-26. These data include Fe and depth. The instruments used to collect these data include Mass Spectrometer and McLane Pump. These data were collected by Mak A. Saito of Woods Hole Oceanographic Institution as part of the "Collaborative Research: Iron and phosphorus balanced limitation of nitrogen fixation in the oligotrophic ocean (TriCoLim)", "Collaborative Research: Evolutionary, biochemical and biogeochemical responses of marine cyanobacteria to warming and iron limitation interactions (Cyanobacteria Warming Responses)", "Collaborative Research: Underexplored Connections between Nitrogen and Trace Metal Cycling in Oxygen Minimum Zones Mediated by Metalloenzyme Inventories (O2 Min Metalloenzyme)", "Connecting Trace Elements and Metalloenzymes Across Marine Biogeochemical Gradients (MetZyme)", "Marine Microbial Investigator Award: Investigator Mak Saito (MM Saito)", "The ProteOMZ Expedition: Investigating Life Without Oxygen in the Pacific Ocean (ProteOMZ (Proteomics in an Oxygen Minimum Zone))", and "US GEOTRACES PMT: Cobalt Biogeochemical Cycling and Connections to Metalloenzymes in the Pacific Ocean (PMT Cobalt and Metalloenzymes)" projects and "U.S. GEOTRACES (U.S. GEOTRACES)" program. The Biological and Chemical Oceanography Data Management Office (BCO-DMO) submitted these data to NCEI on 2020-04-27. The following is the text of the dataset description provided by BCO-DMO: Dataset Description: Nitrite Oxidoreductase targeted metaproteomics from R/V Kilo Moana cruise KM1128 and R/V Falkor cruise FK160115 in the Central Pacific Ocean in 2011 and 2016. NxrA and NxrB peptide concentrations in fmol/L. Peptide names are using the GEOTRACES naming convention (PEP for peptide, full tryptic peptide amino acid sequence, Protein name, Sampling device (=Pump)). Quality flags follow each peptide column and use the GEOTRACES convention of 1 for good, 6 for below detection limit. These data were published in Saito et al., 2020 as Supplementary Table 1. |
| Date received: | 20200427 |
| Start date: | 20111005 |
| End date: | 20160126 |
| Seanames: | |
| West boundary: | 140 |
| East boundary: | -154.4 |
| North boundary: | 17 |
| South boundary: | -3.5 |
| Observation types: | chemical, physical |
| Instrument types: | mass spectrometer |
| Datatypes: | DEPTH - OBSERVATION, Iron |
| Submitter: | |
| Submitting institution: | Biological and Chemical Oceanography Data Management Office |
| Collecting institutions: | Woods Hole Oceanographic Institution |
| Contributing projects: | GEOTRACES |
| Platforms: | Falkor (CIFR), KILO MOANA (33KB) |
| Number of observations: | |
| Supplementary information: | Acquisition Description: Metaproteomics samples were collected by McLane pump onto 0.2 micron Supor membrane filters, with 51 and 3.0 micron prefilters. Global metaproteomic analyses were conducted using 1-dimensional (1D) and 2-dimensional (2D) chromatographic separation for the Metzyme and ProteOMZ expeditions respectively. Following global metaproteomic analyses, targeted metaproteomic assays were designed and samples were analyzed again by parallel reaction monitoring (PRM) mass spectrometry using mass spectral information from the global proteomic analyses. See methods in Saito et al., 2020 Nature Geosciences for full details. Samples were analyzed on a Thermo Fusion Orbitrap mass spectrometer. See methods in Saito et al., 2020 Nature Geosciences for full details. Data quality flags are included following GEOTRACES conventions for results below detection limit (flag= 6). Parameters were named using the prior GEOTRACES IDP parameter naming convention used for peptides (PEP), although these are new parameters not previously submitted here or elsewhere. The peptide parameter naming convention was developed in collaboration with the GEOTRACES program. In other to avoid the sustainability challenge of having to maintain a parameter key of codes that represent protein and peptide sequences, the tryptic peptide amino acid sequences are inserted into the parameter name, with prefixes and suffixes for additional metadata. For example, the parameter name "PEP_MTIQWGK_NxrA_PUMP" has the following components. The prefix PEP refers to the peptides datatype, "MTIQWGK" refers to the specific amino acid sequence of the measured peptide, using the IUPAC-IUB 1 letter amino acid naming convention. This sequence can be used to calculate the molecular weight and elemental formula of the molecule that was measured (e.g. see https://web.expasy.org/compute_pi/ and https://web.expasy.org/protparam/). "NxrA" refers to the protein name, in this case nitrite oxidoreductase subunit A. "PUMP" refers to the samping methodology, in order to differentiate when samples may be collected from the same location and depth but by different methods. This approach is useful as tryptic peptides are short enough in sequence to allow their use within parameter names, and each parameter name uniquely describes the molecule being measured, even when, as in this Nxr study, many different peptides are being measured from within a single protein. Reference: https://febs.onlinelibrary.wiley.com/doi/pdf/10.1111/j.1432-1033.1984.tb07877.x |
| Availability date: | |
| Metadata version: | 1 |
| Keydate: | 2023-05-06 03:50:45+00 |
| Editdate: | 2023-05-06 03:52:12+00 |