PXD025439

PXD025439 is an original dataset announced via ProteomeXchange.

Title	Membrane enriched temperature series proteome of Francisella tularensis subspecies novicida in wild type and lipid A acyltransferase null mutants.
Description	Quantitative proteomics has matured into an established tool and longitudinal proteomic experiments have begun to emerge. However, no effective, simple-to-use differential expression method for longitudinal proteomics data has been released. Typically, such data is noisy, contains missing values, has only few time points and biological replicates. To address this need, we provide a comprehensive evaluation of several existing differential expression methods for high-throughput longitudinal omics data and introduce a new method, Robust longitudinal Differential Expression (RolDE). To evaluate the longitudinal differential expression methods in a real proteomics study setting, we generated and used an experimental membrane enriched longitudinal proteomics data of Francisella tularensis subspecies novicida (Fn). For evaluation of the methods, differential expression between the null mutant and the wild type strains was investigated,while their growth at different temperatures offered a surrogate for the different time points. Technical replicates of the samples were used to form technical replicate datasets analyzed with the different methods to evaluate the reproducibility of the methods. In addition, the Fn dataset with known protein modifications, was used to explore the evaluated methods ability to detect these proteins and other closely associated pathway proteins expected to be affected.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:27:05.226.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Tommi Välikangas
SpeciesList	scientific name: Francisella tularensis subsp. novicida (strain U112); NCBI TaxID: 401614;
ModificationList	acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	LTQ Orbitrap Elite

Revision	Datetime	Status	ChangeLog Entry
0	2021-04-16 06:15:23	ID requested
1	2023-01-24 00:21:57	announced
⏵ 2	2023-11-14 08:27:06	announced	2023-11-14: Updated project metadata.

V, ä, likangas T, Suomi T, Chandler CE, Scott AJ, Tran BQ, Ernst RK, Goodlett DR, Elo LL, Benchmarking tools for detecting longitudinal differential expression in proteomics data allows establishing a robust reproducibility optimization regression approach. Nat Commun, 13(1):7877(2022) [pubmed]

submitter keyword: Francisella tularensis subspecies novicida, lpxD1, lipid A, knockout, lpxD2, Francisella novicida, Orbitrap Elite, temperature series, lpxL,Francisella tularensis

David R. Goodlett
contact affiliation	University of Victoria – Victoria, British Columbia, Canada V8P 3E6; International Centre for Cancer Vaccine Science, Gdansk, Poland
contact email	goodlett@uvic.ca
lab head
Tommi Välikangas
contact affiliation	University of Turku
contact email	tsvali@utu.fi
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD025439
     1. Label: PRIDE project
     2. Name: Membrane enriched temperature series proteome of Francisella tularensis subspecies novicida in wild type and lipid A acyltransferase null mutants.