PXD028927-1

PXD028927 is an original dataset announced via ProteomeXchange.

Title	Normalization of Organ-on-a-Chip Samples for Mass Spectrometry Based Proteomics and Metabolomics via Dansylation-based Assay
Description	Mass spectrometry based ‘omics pairs well with organ-on-a-chip-based investigations, which often have lim-ited cellular material for sampling. However, a common issue with these chip-based platforms is well-to-well or chip-to-chip variability in the proteome and metabolome due to factors such as plate edge effects, cellular asynchronization, ef-fluent flow, and overall limited cell count. This causes high variability in label free quantitative workflows, thus masking true biological changes that occur within the system. Solutions to this problem have been approached via data processing tools and post-acquisition normalization strategies such as constant median, constant sum, and overall signal normaliza-tion. Unfortunately, these methods do not adequately correct for the large variations, resulting in a need for increased biological replicates. The methods in this work utilize a dansylation based assay with a subset of labeled metabolites that allow for pre-acquisition normalization to better correlate the biological perturbations that truly occur in chip-based platforms. This was performed in tandem with a proteomics pipeline employing a BCA protein assay to similarly achieve pre-acquisition normalization. A decreased coefficient of variation percentage is achieved, more significant changes are observed through the proteome and metabolome, and better classification of biological replicates is acquired as a result of these strategies.
HostingRepository	PRIDE
AnnounceDate	2026-01-24
AnnouncementXML	Submission_2026-01-24_00:48:08.229.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Conor Jenkins
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606;
ModificationList	phosphorylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Eclipse

Revision	Datetime	Status	ChangeLog Entry
0	2021-10-04 10:01:53	ID requested
⏵ 1	2026-01-24 00:48:09	announced

10.1016/j.tiv.2022.105540;

Gallagher EM, Rizzo GM, Dorsey R, Dhummakupt ES, Moran TS, Mach PM, Jenkins CC, Normalization of organ-on-a-Chip samples for mass spectrometry based proteomics and metabolomics via Dansylation-based assay. Toxicol In Vitro, 88():105540(2023) [pubmed]

submitter keyword: liver,Organ-on-a-chip, normalization

Conor Chapman Jenkins
contact affiliation	U.S. Army, DEVCOM CBC
contact email	conor.c.jenkins.civ@army.mil
lab head
Conor Jenkins
contact affiliation	US Army DEVCOM CBC
contact email	conor.c.jenkins.civ@army.mil
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD028927
     1. Label: PRIDE project
     2. Name: Normalization of Organ-on-a-Chip Samples for Mass Spectrometry Based Proteomics and Metabolomics via Dansylation-based Assay