PXD063953

PXD063953 is an original dataset announced via ProteomeXchange.

Title	optTMT: optimizing any experimental design to minimize false positives caused by TMT reporter ion interference
Description	Human induced pluripotent stem cell (iPSC) technology holds great potential for therapeutic and research purposes, by providing improved models of disease and for studying mechanisms regulating differentiation. The Human Induced Pluripotent Stem Cell Initiative (HipSci) was established to generate large panel of high-quality human iPSC lines from both healthy donors and disease cohorts for the research community. Here I present a reanalysis of the resource data published by (Kilpinen et al. 2017, Nature) which features a comprehensive proteomic analysis of >200 human iPSC lines obtained from >100 different donors. This dataset has identified in total >16,000 proteins expressed in iPSCs, with expression levels spanning 7 orders of magnitude. Raw files from this dataset were published by (Brenes et al. 2019, Molecular & Cellular Protemics) and can be found on ProteomeXchange with the identifier PXD010557. The ones used for this analysis were corresponding to 21 batches out of the 24 provided by (Brenes et al. 2019, Molecular & Cellular Protemics); their raw files were also deposited in this repository. This reanalysis was performed with the aim to evaluate the impact of TMT reporter ion interference and the impact of TMT quantification corection on it. Each PD results files with the mention '_woQuanCorrection' didn't have any TMT quantification correction applied while the one with the mention '_wQuanCorrection' did. The product data sheet used for applying such correction is the one provided by ThermoFisher Scientific for the TNT10-plex reagent product number 90110, lot number UL298812.
HostingRepository	PRIDE
AnnounceDate	2026-03-05
AnnouncementXML	Submission_2026-03-05_09:13:36.349.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Marc-Antoine Gerault
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606;
ModificationList	TMT6plex-126 reporter+balance reagent acylated residue; acetylated residue; monohydroxylated residue; deamidated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2025-05-14 23:27:42	ID requested
1	2026-02-28 02:35:10	announced
2	2026-03-05 08:29:36	announced	2026-03-05: Updated project metadata.
3	2026-03-05 09:04:34	announced	2026-03-05: Updated project metadata.
⏵ 4	2026-03-05 09:13:36	announced	2026-03-05: Updated project metadata.

10.1093/BIOADV/VBAF243;

submitter keyword: None

Marc-Antoine Gerault
contact affiliation	Karolinska Institutet, Department of Oncology-Pathology, Pär Nordlund's lab Stockholm, SE 171 77
contact email	marc.antoine.gerault@ki.se
lab head
Marc-Antoine Gerault
contact affiliation	Department of Oncology-Pathology, Karolinska Institutet, 171 77 Stockholm, Sweden
contact email	marc.antoine.gerault@ki.se
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/2026/02/PXD063953

PRIDE project URI

• PRIDE
  1. PXD063953
     1. Label: PRIDE project
     2. Name: optTMT: optimizing any experimental design to minimize false positives caused by TMT reporter ion interference