PXD037914 is an
original dataset announced via ProteomeXchange.
Dataset Summary
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 |
Dataset History
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. |
Publication List
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 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 | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD037914
- Label: PRIDE project
- Name: Detection of known and novel small proteins in Pseudomonas stutzeri using a combination of bottom-up and top-down proteomics and proteogenomics