PXD037914

PXD037914 is an original dataset announced via ProteomeXchange.

Title	Detection of known and novel small proteins in Pseudomonas stutzeri using a combination of bottom-up and top-down proteomics and proteogenomics
Description	Here we performed a comprehensive genomic and proteomics analysis of P. stutzeri in aerobic and oxygen-limiting conditions. We combined de novo genome assembly relying on 3rd generation long read sequencing technologies to report the first complete P. stutzeri ATCC14405 genome, which added over 110 kb of sequence and contains 126 full length CDS that were only partially covered in the fragmented short read-based genome assembly available for this strain. With this optimal basis for downstream functional genomics, we next carried out state of the art bottom-up and top-down proteomics analyses to report the most detailed study of proteome remodeling in response to oxygen limitation in P. stutzeri. We identified more than 2900 proteins, i.e. greater than 70% of the theoretical proteome, including 160 annotated small proteins. The proteins included well-established enzymes involved in denitrification and metabolic adaptation to oxygen-limiting conditions, as well as uncharacterized proteins. Notably, we identified 16 novel small proteins that had so far been missed in the genome annotation.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:59:43.612.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD037914
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Julian Langer
SpeciesList	scientific name: Pseudomonas stutzeri ATCC 14405 = CCUG 16156; NCBI TaxID: 32042;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2022-11-03 04:44:21	ID requested
1	2023-08-04 04:42:48	announced
2	2023-11-14 07:01:27	announced	2023-11-14: Updated project metadata.
⏵ 3	2024-10-22 05:59:43	announced	2024-10-22: Updated project metadata.

10.1021/ACS.ANALCHEM.3C00676;

10.6019/PXD037914;

submitter keyword: Pseudomonas, metabolism, small proteome, genome annotation,direct sequencing, top-down proteomics, proteogenomics, novel small proteins, oxygen limitation

Julian D. Langer
contact affiliation	Max Planck Institute of Biophysics Max Planck Institute for Brain Research
contact email	julian.langer@biophys.mpg.de
lab head
Julian Langer
contact affiliation	MPIs for Biophysics and Brain Research
contact email	julian.langer@biophys.mpg.de
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/2023/08/PXD037914

PRIDE project URI

• PRIDE
  1. PXD037914
     1. Label: PRIDE project
     2. Name: Detection of known and novel small proteins in Pseudomonas stutzeri using a combination of bottom-up and top-down proteomics and proteogenomics