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PXD037914

PXD037914 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleDetection of known and novel small proteins in Pseudomonas stutzeri using a combination of bottom-up and top-down proteomics and proteogenomics
DescriptionHere 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.
HostingRepositoryPRIDE
AnnounceDate2024-10-22
AnnouncementXMLSubmission_2024-10-22_05:59:43.612.xml
DigitalObjectIdentifierhttps://dx.doi.org/10.6019/PXD037914
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportSupported dataset by repository
PrimarySubmitterJulian Langer
SpeciesList scientific name: Pseudomonas stutzeri ATCC 14405 = CCUG 16156; NCBI TaxID: 32042;
ModificationListmonohydroxylated residue; iodoacetamide derivatized residue
InstrumentOrbitrap Fusion Lumos
Dataset History
RevisionDatetimeStatusChangeLog Entry
02022-11-03 04:44:21ID requested
12023-08-04 04:42:48announced
22023-11-14 07:01:27announced2023-11-14: Updated project metadata.
32024-10-22 05:59:43announced2024-10-22: Updated project metadata.
Publication List
10.1021/ACS.ANALCHEM.3C00676;
10.6019/PXD037914;
Keyword List
submitter keyword: Pseudomonas, metabolism, small proteome, genome annotation,direct sequencing, top-down proteomics, proteogenomics, novel small proteins, oxygen limitation
Contact List
Julian D. Langer
contact affiliationMax Planck Institute of Biophysics Max Planck Institute for Brain Research
contact emailjulian.langer@biophys.mpg.de
lab head
Julian Langer
contact affiliationMPIs for Biophysics and Brain Research
contact emailjulian.langer@biophys.mpg.de
dataset submitter
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Dataset FTP location
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