PXD053122

PXD053122 is an original dataset announced via ProteomeXchange.

Title	Analytical insights from FFPE-based proteome profiling of 1,200 pan cancer cases
Description	Proteome profiling of formalin-fixed paraffin-embedded (FFPE) specimens has gained traction in recent years for the analysis of human clinical material, notably cancer tissue for the discovery of molecular biomarkers. However, published reports so far focused on certain cancer entities and comprised a limited number of cases. In addition, no in-depth investigation into the long-term performance of experimental workflows for FFPE proteomics has been reported yet. In study, we assessed a previously published workflow in terms of robustness and scalability by analyzing the proteomes of 1,220 tumor specimens from six cancer entities processed over the course of three years. Important analytical insights include the necessity of introducing a new normalization method that ensures equal and reproducible sample loading for LC-MS/MS analysis across cohorts, the benefit of spiking retention time standards to be able to compare samples across extended periods of time, that tumors can, on average, be profiled to a depth of >5,000 proteins within an acceptable time frame and, surprisingly, that current software is unable to process such large data sets simultaneously. Beyond these analytical insights, this study provides protein expression information on 11,000 proteins in >1,200 tumor samples from six cancer entities representing the first comprehensive pan-cancer proteome resource for FFPE material to date. The authors believe that the current study provides useful guidance for planning large-scale FFPE proteome projects and is also of immediate utility to the scientific community as the data is publicly accessible via a custom-built ShinyApp enabling a wide range of analysis. This includes e. g. the quantitative comparison of proteins of interest between patients or cohorts or the discovery of protein fingerprints that represent the tissue of origin and proteins that are enriched in certain cancer entities.
HostingRepository	MassIVE
AnnounceDate	2024-10-16
AnnouncementXML	Submission_2024-10-16_07:27:55.611.xml
DigitalObjectIdentifier
ReviewLevel	Non peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Stephan Eckert
SpeciesList	scientific name: Homo sapiens; common name: human; NCBI TaxID: 9606;
ModificationList	Oxidation; Acetyl; Carbamidomethyl
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2024-06-14 05:15:55	ID requested
⏵ 1	2024-10-16 07:27:55	announced

no publication

submitter keyword: FFPE, pan-cancer, DLBCL, OSCC, PDAC, CRC, Glioma, Melanoma, FAIMS, proteomics, large-scale, clinical proteomics, cancer, expression profiles

Bernhard Kuster
contact affiliation	Technical University of Munich (TUM)
contact email	kuster@tum.de
lab head
Stephan Eckert
contact affiliation	Technical University Munich (TUM)
contact email	stephan.eckert@tum.de
dataset submitter

MassIVE dataset URI

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