PXD054975

PXD054975 is an original dataset announced via ProteomeXchange.

Title	Proteomics and phosphoproteomics analysis of Haematococcus pluvialis: An improved method to generate and interpret proteomics and phosphoproteomics data of a non-model species
Description	Haematococcus pluvialis is a green microalga of commercial interests due to its ability to produce a high value ketocarotenoid, astaxanthin. As a non-model species that lacks a well annotated genome, omics analyses such as transcriptomics and proteomics analysis have often been used together with physiological and biochemical analysis to explore pathways of interest. However, interpretation of these datasets remains challenging. In this work, TMT-based proteomics and phosphoproteomics analyses were conducted on Haematococcus cells grown under favorable conditions (green stage biomass) and high-light stress conditions (red stage biomass). Phosphoproteins were enriched using titanium dioxide before LC-MS/MS analysis. Our proteomics and phosphoproteomics analyses identified 1394 proteins and 569 phosphosites on 366 phosphoproteins, respectively. Of these, 1315 proteins and 396 phosphosites on 314 phosphoproteins were quantifiable, among which 370 proteins and 121 phosphosites on 94 phosphoproteins were differentially expressed. Using an improved analysis pipeline that combines Blast2GO, KEGG, and DAVID to analyze differentially expressed proteins and phosphoproteins, total identified proteins increased from 255 to 322 and total identified phosphoproteins increased from 59 to 70, which were 26.28% and 18.64%, respectively, higher than with the UniProt analysis alone. Using this pipeline, a previously uncharacterized protein and phosphoprotein were identified as an ATPase subunit B and a phosphofructokinase, respectively, and further confirmed with translated genomic and transcriptomic data. This work provides the first example of phosphoproteomics analysis in H. pluvialis, while the proteomics and phosphoproteomics analysis pipelines described here may be useful to analyze omics data from other non-model algal species.
HostingRepository	PRIDE
AnnounceDate	2024-11-20
AnnouncementXML	Submission_2024-11-20_12:06:09.850.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Kyarii Ramarui
SpeciesList	scientific name: Haematococcus lacustris; NCBI TaxID: 44745;
ModificationList	phosphorylated residue; acetylated residue; deamidated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2024-08-17 14:56:25	ID requested
⏵ 1	2024-11-20 12:06:10	announced

Dataset with its publication pending

submitter keyword: TMT,Haematococcus pluvialis, LC-MS/MS

Yantao Li
contact affiliation	University of Maryland Center for Environmental Science -- Institute of Marine and Environmental Technology and University of Maryland, Baltimore County, United States
contact email	yantao@umces.edu
lab head
Kyarii Ramarui
contact affiliation	University of Maryland Center for Environmental Science -- Institute of Marine and Environmental Technology
contact email	kramarui@umces.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD054975
     1. Label: PRIDE project
     2. Name: Proteomics and phosphoproteomics analysis of Haematococcus pluvialis: An improved method to generate and interpret proteomics and phosphoproteomics data of a non-model species