Dataset Information

Structural surfaceomics of myeloma models to identify tumor-specific protein conformations

ABSTRACT: Proteins at the cell surface are promising targets for cancer immunotherapies. While standard surface proteomics can be powerful for target discovery, even more fruitful is identifying cancer-specific surface protein features. To this end, we recently described a technology to identify cancer-specific protein three-dimensional conformations. In “structural surfaceomics”, we integrated XL-MS and surface protein biotinylation to identify the active conformation of integrin beta-2 as a promising cellular therapy target in acute myeloid leukemia (Mandal et al, Nature Cancer (2023)). However, we only applied structural surfaceomics to a single cancer model, and crosslink modeling was done manually. Here, we apply our technology to additional cancer models and implement an automated pipeline for crosslink characterization, AlphaCross-XL (Biswas et al, ASMS abstract (2023)).

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): B Cell, Permanent Cell Line Cell, Cell Culture

DISEASE(S): Prostate Adenocarcinoma,Plasmacytoma

SUBMITTER: Abhilash Barpanda

LAB HEAD: Arun Wiita

PROVIDER: PXD059495 | Pride | 2025-10-20

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	20250325_amo1_PhoX_fraction12.raw	Raw
	20250325_amo1_PhoX_fraction15.raw	Raw
	20250325_amo1_PhoX_fraction18.raw	Raw
	20250325_amo1_PhoX_fraction21.raw	Raw
	20250325_amo1_PhoX_fraction50.raw	Raw

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Publications

AlphaCross-XL: A Seamless Tool for Automated and Proteome-Scale Mapping of Cross-Linked Peptides Onto 3D Protein Structures.

Shenoy Sanjyot Vinayak SV Biswas Deeptarup D Zalevsky Arthur A Kishishita Audrey A Verma Ayushi A Upadhay Ishan I He Yi Y Sali Andrej A Viner Rosa R Mandal Kamal K Srivastava Sanjeeva S Wiita Arun P AP

Molecular & cellular proteomics : MCP 20250819 10

Crosslinking mass spectrometry (XL-MS) is an exciting proteomics technology to capture native protein conformations in real time within biological systems. Historically, however, implementation of this technology has typically been limited to single purified recombinant proteins or in vitro-assembled protein complexes. These limitations are associated with inherent challenges in XL-MS analysis, including extremely low abundance of crosslinked (XL) peptides and complex deconvolution of XL peptide ...[more]

PMID: 40840759

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