PXD022112 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | Harnessing machine learning to unravel protein degradation in Escherichia coli |
Description | Degradation of intracellular proteins in Gram-negative bacteria regulates various cellular processes and serves as a quality control mechanism by eliminating damaged proteins. To understand what causes the proteolytic machinery of the cell to degrade some proteins while sparing others, we employed a quantitative pulsed-SILAC (Stable Isotope Labeling with Amino acids in Cell culture) method followed by mass spectrometry analysis to determine the half-lives for the proteome of exponentially growing Escherichia coli, under standard conditions. We developed a likelihood-based statistical test to findactively degraded proteins, and identified dozens of novel proteins that are fast-degrading. Finally, we used structural, physicochemical and protein-protein interaction network descriptorsto train a machine-learning classifier to discriminate fast-degrading proteins from the rest of the proteome. Our combined computational-experimental approach provides means for proteomic-based discovery of fast degrading proteins in bacteria and the elucidation of the factors determining protein half-livesand have implications for protein engineering. Moreover, as rapidly degraded proteins may play an important role in pathogenesis, our findings could identify new potential antibacterial drug targets |
HostingRepository | PRIDE |
AnnounceDate | 2021-01-13 |
AnnouncementXML | Submission_2021-01-12_23:48:58.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | Meital Kupervaser |
SpeciesList | scientific name: Escherichia coli; NCBI TaxID: 562; |
ModificationList | monohydroxylated residue; iodoacetamide derivatized residue |
Instrument | Q Exactive HF |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2020-10-21 02:34:00 | ID requested | |
⏵ 1 | 2021-01-12 23:48:58 | announced | |
Publication List
Dataset with its publication pending |
Keyword List
submitter keyword: Protein Degradation, Proteomics, Machine Learning, SILAC |
Contact List
Tal Pupko |
contact affiliation | Shmunis School for Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel |
contact email | talp@tauex.tau.ac.il |
lab head | |
Meital Kupervaser |
contact affiliation | Weizmann Institute of Science |
contact email | meital.kupervaser@weizmann.ac.il |
dataset submitter | |
Full Dataset Link List
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD022112
- Label: PRIDE project
- Name: Harnessing machine learning to unravel protein degradation in Escherichia coli