PXD053122
PXD053122 is an original dataset announced via ProteomeXchange.
Dataset Summary
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 |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
---|---|---|---|
0 | 2024-06-14 05:15:55 | ID requested | |
⏵ 1 | 2024-10-16 07:27:55 | announced |
Publication List
no publication |
Keyword List
submitter keyword: FFPE, pan-cancer, DLBCL, OSCC, PDAC, CRC, Glioma, Melanoma, FAIMS, proteomics, large-scale, clinical proteomics, cancer, expression profiles |
Contact List
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 |
Full Dataset Link List
MassIVE dataset URI |
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://massive.ucsd.edu/v08/MSV000095036/ |