PXD062642-1

PXD062642 is an original dataset announced via ProteomeXchange.

Title	A transcriptomic and proteomic map of primary human cell types
Description	Molecular profiling of human primary cell types is essential for a comprehensive understanding of human biology. Here, we describe the transcriptome and proteome map of 28 primary human cell types. Three major clusters of epithelial, endothelial, and mesenchymal cell types were observed at both the transcriptome and proteome levels along with the discovery of cell type specific molecules including GRAP and C1orf116. Among them, we further validated the expression of a novel epithelial cell specific protein C1orf116 using immunohistochemistry across a range of human tissues. An exhaustive protein database search considering 39 different post-translational modifications (PTMs) provided new insights into the PTM landscape of primary cells. This approach enabled the identification of previously understudied PTMs such as serine O-acetylation and histidine methylation, while also providing comprehensive characterization of proteins with diverse PTM types. Interestingly, the unexpectedly higher frequency of dioxidation on tryptophan compared to methionine led us to characterize oxidative mitochondria complex subunit proteins modified through oxidative phosphorylation in mitochondria. Further, a unique protein database search strategy that considered alternative translational start sites, splice junctions and translational readthrough provided an opportunity to refine genome annotation using proteomic evidence. As an example, several peptides derived from translational readthrough were detected including extended sequence of LDHB and MDH1, which is the first report with peptide level evidence for these proteins. We believe that our data with an extensive catalog of the transcriptome and proteome of normal human primary cells will provide unique insights into cell biology revealing cellular heterogeneity and cell type-specific molecular cues. These insights could have a broad impact of pathophysiology of disease mechanisms that were missed by tissue proteomics.
HostingRepository	PRIDE
AnnounceDate	2026-01-24
AnnouncementXML	Submission_2026-01-24_05:49:52.955.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Akhilesh Pandey
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606;
ModificationList	monomethylated residue; dihydroxylated residue; phosphorylated residue; acetylated residue; monohydroxylated residue; deamidated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2025-04-05 14:00:14	ID requested
⏵ 1	2026-01-24 05:49:54	announced

10.1093/nar/gkaf1498;

Mun DG, Madugundu AK, Renuse S, Nirujogi RS, Na CH, Kim MS, Saraswat M, Singh S, Ramarajan MG, Tiwary S, Cox J, Prakash A, Halushka MK, Burns KH, Kandasamy RK, Pandey A, A transcriptomic and proteomic map of primary human cell types. Nucleic Acids Res, 54(2):(2026) [pubmed]

submitter keyword: Primary cells, post-translational modifications, transcriptomics, LC-MS/MS

Akhilesh Pandey
contact affiliation	Department of Laboratory Medicine and Pathology, Mayo Clinic
contact email	pandey.akhilesh@mayo.edu
lab head
Akhilesh Pandey
contact affiliation	Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905
contact email	pandey.akhilesh@mayo.edu
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/2026/01/PXD062642

PRIDE project URI

• PRIDE
  1. PXD062642
     1. Label: PRIDE project
     2. Name: A transcriptomic and proteomic map of primary human cell types