HOT311_proteomics_databases_WaldbauerLab

Published: 25 March 2022| Version 1 | DOI: 10.17632/7226j6cpp3.1
Contributors:
Amy Zimmerman,

Description

Databases associated with 15N-tracking proteomics of nitrogen allocation in surface ocean microbial community

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Metatranscriptomes from (Vislova et al., 2019) and (Ottesen et al., 2014) were downloaded from the Sequence Read Archive, translated with FragGeneScan, trimmed to have tryptic ends, and de-replicated to contain only unique sequences. A list of peptides identified in unamended and 14N-amended samples was used to subset the primary search database (dbVislova-Ottesen.deduped.trim.faa) to only include translated protein sequences that contained exact amino acid sequence matches to an observed peptide (dbVislova-Ottesen-deduped-trim_unlab-PSM_subset.fasta). This process reduced the database for 15N peptide searches from 10,854,086 sequences (397,730,209 residues) to 225,053 sequences (12,195,544 residues). A. Vislova, O. A. Sosa, J. M. Eppley, A. E. Romano, E. F. DeLong, Diel Oscillation of Microbial Gene Transcripts Declines With Depth in Oligotrophic Ocean Waters. Front. Microbiol. 10, 2191 (2019). E. A. Ottesen, C. R. Young, S. M. Gifford, J. M. Eppley, R. Marin, S. C. Schuster, C. A. 5 Scholin, E. F. DeLong, Multispecies diel transcriptional oscillations in open ocean heterotrophic bacterial assemblages. Science. 345, 207–212 (2014).

Institutions

University of Chicago

Categories

Proteomics, Environmental Microbiology, Nutrient Uptake

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