PXD007254 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | Protein Abundances can Distinguish Between Naturally-occurring and Laboratory Strains of Yersinia pestis, the Causative Agent of Plague |
Description | The rapid pace of bacterial evolution enables organisms to adapt to the laboratory environment with repeated passage and thus diverge from naturally-occurring environmental (“wild”) strains. Distinguishing wild and laboratory strains is clearly important for biodefense and bioforensics; however, DNA sequence data alone has thus far not provided a clear signature, perhaps due to lack of understanding of how diverse genome changes lead to convergent phenotypes, difficulty in detecting certain types of mutations, or perhaps because some adaptive modifications are epigenetic. Monitoring protein abundance, a molecular measure of phenotype, can overcome some of these difficulties. We have assembled a collection of Yersinia pestis proteomics datasets from our own published and unpublished work, and from a proteomics data archive, and demonstrated that protein abundance data can clearly distinguish laboratory-adapted from wild. We developed a lasso logistic regression classifier that uses binary (presence/absence) or quantitative protein abundance measures to predict whether a sample is laboratory-adapted or wild that proved to be ~98% accurate, as judged by replicated 10-fold cross-validation. Protein features selected by the classifier accord well with our previous study of laboratory adaptation in Y. pestis. The input data was derived from a variety of unrelated experiments and contained significant confounding variables. We show that the classifier is robust with respect to these variables. The methodology is able to discover signatures for laboratory facility and culture medium that are largely independent of the signature of laboratory adaptation. Going beyond our previous laboratory evolution study, this work suggests that proteomic differences between laboratory-adapted and wild Y. pestis are general, potentially pointing to a process that could apply to other species as well. Additionally, we show that proteomics datasets (even archived data collected for different purposes) contain the information necessary to distinguish wild and laboratory samples. This work has clear applications in biomarker detection as well as biodefense. |
HostingRepository | PRIDE |
AnnounceDate | 2024-10-22 |
AnnouncementXML | Submission_2024-10-22_04:13:13.779.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | Owen Leiser |
SpeciesList | scientific name: Yersinia pestis KIM D27; NCBI TaxID: 687916; scientific name: Yersinia pestis CO92; NCBI TaxID: 214092; |
ModificationList | acetylated residue; iodoacetamide derivatized residue |
Instrument | LTQ Orbitrap |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2017-08-11 08:05:48 | ID requested | |
1 | 2017-09-08 00:24:19 | announced | |
⏵ 2 | 2024-10-22 04:13:14 | announced | 2024-10-22: Updated project metadata. |
Publication List
Merkley ED, Sego LH, Lin A, Leiser OP, Kaiser BLD, Adkins JN, Keim PS, Wagner DM, Kreuzer HW, Protein abundances can distinguish between naturally-occurring and laboratory strains of Yersinia pestis, the causative agent of plague. PLoS One, 12(8):e0183478(2017) [pubmed] |
10.1371/journal.pone.0183478; |
Keyword List
curator keyword: Biological |
submitter keyword: machine learning, evolution, laboratory adaptation,Yersinia pestis |
Contact List
Helen Kreuzer |
contact affiliation | Pacific Northwest National Laboratory |
contact email | Helen.Kreuzer@pnnl.gov |
lab head | |
Owen Leiser |
contact affiliation | Pacific Northwest National Laboratory |
contact email | Owen.Leiser@pnnl.gov |
dataset submitter | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD007254
- Label: PRIDE project
- Name: Protein Abundances can Distinguish Between Naturally-occurring and Laboratory Strains of Yersinia pestis, the Causative Agent of Plague