Proteomics

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Proteome-scale recombinant standard datasets for XL-MS

ABSTRACT: This submission includes the complete set of raw data generated from the analytical standard, the concept of which is described in our manuscript "Proteome-Scale Recombinant Standards And A Robust High-Speed Search Engine To Advance Cross-Linking MS-Based Interactomics". In this study, we develop a strategy to generate a well-controlled XL-MS standard by systematically mixing and cross-linking recombinant proteins. The standard can be split into independent datasets, each of which has the MS2-level complexity of a typical proteome-wide XL-MS experiment. This submission includes 5 raw datasets (batches 1-5), each comprising 64 randomly selected human proteins engaging in up to 224 allowed protein-protein interactions per dataset. The data were searched with Scout (v. 1.4.14, https://github.com/diogobor/Scout) and results are reported in mzIdentML 1.2.0 format. For the specific results reported in our original publication, please refer to PXD042173.

INSTRUMENT(S): Orbitrap Fusion Lumos

ORGANISM(S): Homo Sapiens (human) Escherichia Coli

SUBMITTER: Diogo Borges Lima  

LAB HEAD: Fan Liu

PROVIDER: PXD042173 | Pride | 2024-08-06

REPOSITORIES: Pride

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Dataset's files

Source:
Action DRS
L1_20210727_MxR_FDR_firstbatch_DSSOplate2_B12.raw Raw
L1_20210727_MxR_FDR_firstbatch_DSSOplate2_E12.raw Raw
L1_20210727_MxR_FDR_firstbatch_DSSOplate2_H12.raw Raw
L1_20210806_MxR_FDR_firstbatch_DSSOplate_C10.raw Raw
L1_20210806_MxR_FDR_firstbatch_DSSOplate_C11.raw Raw
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Publications

Proteome-scale recombinant standards and a robust high-speed search engine to advance cross-linking MS-based interactomics.

Clasen Milan Avila MA   Ruwolt Max M   Wang Cong C   Ruta Julia J   Bogdanow Boris B   Kurt Louise U LU   Zhang Zehong Z   Wang Shuai S   Gozzo Fabio C FC   Chen Tao T   Carvalho Paulo C PC   Lima Diogo Borges DB   Liu Fan F  

Nature methods 20241031 12

Advancing data analysis tools for proteome-wide cross-linking mass spectrometry (XL-MS) requires ground-truth standards that mimic biological complexity. Here we develop well-controlled XL-MS standards comprising hundreds of recombinant proteins that are systematically mixed for cross-linking. We use one standard dataset to guide the development of Scout, a search engine for XL-MS with MS-cleavable cross-linkers. Using other, independent standard datasets and published datasets, we benchmark the  ...[more]

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