Dataset Information

Effect of cadmium in the microalga Chlorella sorokiniana: A proteomic study

ABSTRACT: Effect of cadmium in the microalga Chlorella sorokiniana

INSTRUMENT(S): TripleTOF 5600

ORGANISM(S): Chlorella Sp. Sag 211-18

TISSUE(S): Photosynthetic Cell

SUBMITTER: Luis C. Romero

LAB HEAD: Romero, LC

PROVIDER: PXD015932 | Pride | 2020-10-05

REPOSITORIES: Pride

ACCESS DATA

Dataset's files

Source:

			Action	DRS
	DataanalysisSWATH.xlsx	Xlsx
	Libreria_Cd_JVigara_04_02_19.group	Other
	Libreria_Cd_JVigara_04_02_19.mgf	Mgf
	Libreria_Control_JVigara_04_02_19.group	Other
	Libreria_Control_JVigara_04_02_19.mgf	Mgf

Items per page:

1 - 5 of 60

Publications

Effect of cadmium in the microalga Chlorella sorokiniana: A proteomic study.

León-Vaz Antonio A Romero Luis C LC Gotor Cecilia C León Rosa R Vigara Javier J

Ecotoxicology and environmental safety 20200917

Cadmium is one of the most common heavy metals in contaminated aquatic environments and one of the most toxic contaminants for phytoplankton. Nevertheless, there are not enough studies focused on the effect of this metal in algae. Through a proteomic approach, this work shows how Cd can alter the growth, cell morphology and metabolism of the microalga Chlorella sorokiniana. Using the sequential window acquisition of all theoretical fragment ion spectra mass spectrometry (SWATH-MS), we concluded ...[more]

PMID: 32949933

Similar Datasets

Project description:Chronic lymphocytic leukaemia (CLL) is renowned for its variable clinical course and response to therapy, suggesting a role for precision medicine. However, the molecular basis of CLL variability remains incompletely understood. Recent developments in data independent acquisition (DIA) -MS technologies, such as SWATH (Sequential Windowed Acquisition of all THeoretical fragments), provide an opportunity to study the pathophysiology of CLL at the proteome level. This report describes the sample replication and data handling requirements for SWATH-MS analysis of clinical samples. A CLL-specific spectral library compromising over 1,500,000 spectra with digital information for over 150,000 peptides has been generated to enable the quantification of up to 7736 proteins. To assess the reproducibility of the assay, SWATH-MS analysis was performed on 6 cryopreserved CLL patient samples, incorporating biological (IGHV mutational status), sample preparation and MS technical replicates. Quantitative information was obtained for 5169 proteins (<1% FDR) across 54 SWATH-MS acquisitions. These analyses showed that SWATH-MS is a highly reproducible technique. However, replicate sample preparations on different days was identified as the main source of variation. To overcome the effect of variation between sample preparation batches, different computational approaches for batch correction were tested. All approaches successfully removed technical variability whilst retaining proteomic differences between clinical subgroups. Functional enrichment analysis of proteins associated to IGHV mutational status highlighted the importance of metabolic remodelling in the biology of CLL and overlapped significantly with previous studies based on gene expression profiling. Finally, an approach to perform statistical power analysis in proteomics studies was developed. This approach could be used to drive the design of future CLL SWATH-MS studies. These fundamental requirements for DIA approaches should be widely applicable to other clinical proteomics studies.