PXD011515

PXD011515 is an original dataset announced via ProteomeXchange.

Title	InfectERA: Challenges in clinical metaproteomics highlighted by the analysis of acute leukemia patients with gut colonization by multidrug-resistant Enterobacteriaceae
Description	The microbiome has a strong impact on human health and disease and is therefore increasingly studied in a clinical context. Metaproteomics is also attracting considerable attention and such data can be efficiently generated today owing to improvements in mass spectrometry based proteomics. As we will discuss in this study, there are still major challenges notably in data analysis that need to be overcome. Here, we analyzed 212 fecal samples from 56 hospitalized acute leukemia patients with multidrug-resistant Enterobactericeae (MRE) colonization using metagenomics and metaproteomics. This is one of the largest clinical metaproteomic studies to date and the first addressing the gut microbiome in MRE colonized acute leukemia patients. Based on this substantial data set, we discuss major current limitations in clinical metaproteomic data analysis to provide guidance to researchers in the field. Notably, the results show that public metagenome databases are incomplete and that sample-specific metagenomes improve results. Furthermore, biological variation is tremendous which challenges clinical study designs and argues that longitudinal measurements of individual patients are a valuable addition to the analysis of patient cohorts.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:51:26.585.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Julia Woortman
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	carbamoylated residue; acetylated residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2018-10-30 02:22:14	ID requested
1	2019-01-14 00:52:03	announced
⏵ 2	2024-10-22 04:51:28	announced	2024-10-22: Updated project metadata.

Rechenberger J, Samaras P, Jarzab A, Behr J, Frejno M, Djukovic A, Sanz J, Gonz, á, lez-Barber, á EM, Salavert M, L, ó, pez-Hontangas JL, Xavier KB, Debrauwer L, Rolain JM, Sanz M, Garcia-Garcera M, Wilhelm M, Ubeda C, Kuster B, Challenges in Clinical Metaproteomics Highlighted by the Analysis of Acute Leukemia Patients with Gut Colonization by Multidrug-Resistant Enterobacteriaceae. Proteomes, 7(1):(2019) [pubmed]

10.3390/proteomes7010002;

curator keyword: Biomedical

submitter keyword: proteomics, multi-omics,Human gut microbiome, metaproteome, mass spectrometry, clinical proteomics, data analysis, multidrug-resistant Enterobacteriaceae

Bernhard Kuster
contact affiliation	Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
contact email	kuster@tum.de
lab head
Julia Woortman
contact affiliation	Chair of Proteomics and Bioanlytics, Technical University of Munich
contact email	julia.rechenberger@tum.de
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/01/PXD011515

PRIDE project URI

• PRIDE
  1. PXD011515
     1. Label: PRIDE project
     2. Name: InfectERA: Challenges in clinical metaproteomics highlighted by the analysis of acute leukemia patients with gut colonization by multidrug-resistant Enterobacteriaceae