⮝ Full datasets listing
PXD073411
PXD073411 is an original dataset announced via ProteomeXchange.
Dataset Summary
| Title | ShapeUpLMD: An Automated Pipeline for Spatially Optimized Laser Microdissection in Multi-omic Tissue Profiling |
| Description | Laser microdissection (LMD) enables enrichment of defined cellular populations from heterogeneous tissues, providing histologically-resolved molecular profiles with spatial resolution. However, the absence of standardized methods for generating optimized regions of interest (ROIs) limits reproducibility and scalability for spatial multi-omic workflows. To address this gap, we developed ShapeUpLMD, an open-source software tool and integrated workflow that automates the optimization of spatially defined ROIs for LMD, directly from digital pathology annotations. Fresh-frozen uterine serous carcinoma (USC) tumors (n = 11) were sectioned onto polyethylene naphthalate slides, scanned and subsequently annotated by an expert pathologist. Tumor and non-tumor ROIs were used to train tumor-specific classifiers in HALO (Indica Labs). Classified tumor or unbiased whole tissue ROIs were refined and optimized by ShapeUpLMD prior to automated collection on a Leica LMD7 microscope. Across the cohort, predicted tumor ROIs increased effective tumor purity by 86 +/- 6% relative to whole tissue while maintaining high spatial concordance between predicted and collected ROIs (accuracy = 0.9 +/- 0.05). Data-independent acquisition mass spectrometry quantified >6500 proteins across spatially resolved ROIs, revealing regionally coherent clustering of adjacent tumor regions and abundance patterns consistent with tumor and non-tumor cell admixture in an unbiased spatial proteomic application. ShapeUpLMD provides an automated, reproducible, and scalable framework that bridges digital pathology with LMD enabling high-fidelity spatial enrichment for multi-omic analyses. This workflow increases throughput, reduces inter-operator variability, and supports standardized, regionally resolved tissue collection for spatial systems biology applications. The software is available at https://github.com/GYNCOE/ShapeUpLMD. |
| HostingRepository | MassIVE |
| AnnounceDate | 2026-09-03 |
| AnnouncementXML | Submission_2026-09-03_12:28:42.649.xml |
| DigitalObjectIdentifier | |
| ReviewLevel | Non peer-reviewed dataset |
| DatasetOrigin | Original dataset |
| RepositorySupport | Unsupported dataset by repository |
| PrimarySubmitter | Gynecologic Cancer Center of Excellence |
| SpeciesList | scientific name: Homo sapiens; common name: human; NCBI TaxID: 9606; |
| ModificationList | Oxidation |
| Instrument | Orbitrap Astral; timsTOF Ultra 2 |
Dataset History
| Revision | Datetime | Status | ChangeLog Entry |
|---|---|---|---|
| 0 | 2026-01-22 07:00:12 | ID requested | |
| ⏵ 1 | 2026-09-03 12:28:43 | announced |
Publication List
| no publication |
Keyword List
| submitter keyword: laser microdissection, spatial multi-omics, spatial proteomics, uterine serous carcinoma, DatasetType:Proteomics |
Contact List
| Thomas P. Conrads | |
|---|---|
| contact affiliation | Women's Health Integrated Research Center |
| contact email | conrads@whirc.org |
| lab head | |
| Gynecologic Cancer Center of Excellence | |
| contact affiliation | Uniformed Services University of the Health Sciences |
| contact email | batemann@whirc.org |
| 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-ftp.ucsd.edu/v12/MSV000100553/ |
