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PXD022112 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleHarnessing machine learning to unravel protein degradation in Escherichia coli
DescriptionDegradation 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
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterMeital Kupervaser
SpeciesList scientific name: Escherichia coli; NCBI TaxID: 562;
ModificationListmonohydroxylated residue; iodoacetamide derivatized residue
InstrumentQ Exactive HF
Dataset History
RevisionDatetimeStatusChangeLog Entry
02020-10-21 02:34:00ID requested
12021-01-12 23:48:58announced
Publication List
Dataset with its publication pending
Keyword List
submitter keyword: Protein Degradation, Proteomics, Machine Learning, SILAC
Contact List
Tal Pupko
contact affiliationShmunis School for Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
contact emailtalp@tauex.tau.ac.il
lab head
Meital Kupervaser
contact affiliationWeizmann Institute of Science
contact emailmeital.kupervaser@weizmann.ac.il
dataset submitter
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