2020, Glen Wheeler, The Marine Biological Association of the UK (MBA) Coccolithus braarudii life cycle protein mass spectrometry
Coccolithophores are crucial for marine biogeochemical cycling. However, much of their physiology remains poorly understood, particularly their elusive haplo-diplontic life cycle. We aimed to characterise differences between HET and HOL Coccolithus braarudii by carrying out protein mass spectrometry of both life phases. We found that the proteome was substantially different and characterized novel physiological mechanisms.
dataset
http://doi.org/10.17031/65afd01b4e0e2
name: DOI link
description: A link to the web service or dataset
name: DASSH Website
description: A link to the general host site
DASSHDT00000529
http://dassh.ac.uk
eng
urn:ogc:def:crs:EPSG::4326
biota
revision
2008-01-06
creation
2011-07-06
revision
2009-11-16
-4.1398
-4.1382
50.3647
50.3638
2020-07-01
2021-04-01
publication
2024-02-01
creation
2021-04-01
revision
2021-04-01
notPlanned
Coccolithophore culturing, harvesting, and protein extraction - Haploid and diploid cultures of C. braarudii were cultured at 15 degrees celsius and harvested during mid-exponential growth. Proteins were extracted using RIPA buffer and liquid nitrogen grinding. Coccolithophore protein mass spectrometry (MS) - TMT labelling, Liquid Chromatography Mass Spectrometry and subsequent raw data analysis were carried out by the Proteomics Facility of Bristol University, UK. The raw data files were processed and quantified using Proteome Discoverer software v2.1 (Thermo Scientific) and searched against the latest release version 2021_2 of the C. braarudii predicted protein database (25204 proteins) from Uniprot (www.uniprot.org), and a common contaminates database using the SEQUEST HT algorithm. The reverse database search option was enabled, and all data was filtered to satisfy false discovery rate (FDR) of 5 percent, which is classed as FDR confidence = Medium. Data were normalized to the total peptide amount in each sample by Proteome Discoverer to equalize peptide abundances across all TMT channels and correcting for differences in sample loading. Normalized proteins were subsequently quality controlled. Differential abundance between life phases was assessed using LIMMA (Ritchie et al., 2015), with a significance level of less than 0.05. Notes on the data spreadsheet - Accession: Uniprot Accession Number for Coccolithus braarudii logFC, AveExpr, t, P.Value, adj.P.Val, B - For information on analysing RNAseq or protein MS data, see package LIMMA: https://kasperdanielhansen.github.io/genbioconductor/html/limma.html Unique Peptides - Number of unique peptide for each protein Protein FDR Confidence: False discovery rate (FDR), 5 percent = Medium, 1 percent = High Blast2GO - Protein annotation Description - Protein description from Uniprot Best BLAST hit and e value: NCBI Blast hit with highest e-value
CC BY
open access
Marine Biological Association of the United Kingdom
originator
Data Manager
Data Archive for Seabed Species and Habitats (DASSH)
Marine Biological Association of the UK, The Laboratory, Citadel Hill
Plymouth
PL1 2PB
01752 633102
01752 633291
custodian
Data Manager
Data Archive for Seabed Species and Habitats (DASSH)
Marine Biological Association of the UK, The Laboratory, Citadel Hill
Plymouth
PL1 2PB
01752 633102
01752 633291
pointOfContact
2024-02-02