PXD033243

PXD033243 is an original dataset announced via ProteomeXchange.

Title	Deep proteogenomics of a unicellular cyanobacterium
Description	Cyanobacteria are photoautotrophs that profoundly impact the biogeochemical cycles on Earth. Due to their photosynthetic lifestyle that includes the fixation of atmospheric CO2, they are of increasing interest for a sustainable economy. Knowledge of protein expression and regulation is key for understanding of the cyanobacterial metabolism; however, proteome studies in cyanobacteria are still limited and cover only a fraction of the theoretical proteome. Here, we performed a proteogenomic analysis of 628 LC-MS/MS measurements for the unicellular model cyanobacterium Synechocystis sp. PCC 6803 to characterize the expressed (phospho)proteome, re-annotate known and discover potential novel open reading frames (ORFs). By mapping extensive shotgun MS proteomics data generated by the SCyCode consortium onto a six-frame translation of the Synechocystis genome, we re-annotated 96 start sites and discovered 103 novel open reading frames (ORFs). Through re-analysis of previously published multi-omics datasets, we confirmed 48 re-annotated or novel ORFs with high confidence. Our study resulted in the largest reported proteome and phosphoproteome dataset for Synechocystis, covering expression of about 80% of the theoretical proteome and 642 O-phosphorylation events under various cultivation conditions, such as nitrogen or carbon limitation. This dataset will serve as a resource providing dedicated information on condition-dependent protein expression and phosphorylation.
HostingRepository	PRIDE
AnnounceDate	2024-01-06
AnnouncementXML	Submission_2024-01-05_20:42:45.364.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Nicolas Nalpas
SpeciesList	scientific name: Synechocystis sp. PCC 6803 substr. PCC-P; NCBI TaxID: 1080230;
ModificationList	phosphorylated residue
Instrument	Q Exactive HF; Orbitrap Exploris 480; Q Exactive HF-X; LTQ Orbitrap Elite

Revision	Datetime	Status	ChangeLog Entry
0	2022-04-14 05:29:51	ID requested
⏵ 1	2024-01-05 20:42:45	announced

10.1021/ACS.JPROTEOME.3C00065;

submitter keyword: primary metabolism, proteogenomics, photosynthesis,cyanobacteria, protein phosphorylation, Synechocystis sp. PCC 6803, small proteins, gene expression, stress acclimation

Boris Macek
contact affiliation	Quantitative proteomics University of Tuebingen Auf der Morgenstelle 15 72076 Tuebingen Germany
contact email	boris.macek@uni-tuebingen.de
lab head
Nicolas Nalpas
contact affiliation	Tuebingen University
contact email	nalpas.nicolas@gmail.com
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2024/01/PXD033243

PRIDE project URI

• PRIDE
  1. PXD033243
     1. Label: PRIDE project
     2. Name: Deep proteogenomics of a unicellular cyanobacterium