Proteomics

Dataset Information

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Dataset used to guide the development of Scout and bechmark XL-MS search engines

ABSTRACT: This submission includes the raw data analyzed and search results 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. The raw datasets included in this submission were used to (1) guide the development of Scout, a machine learning-based search engine for XL-MS with MS-cleavable cross-linkers (batch 1), test different LC-MS acquisition methods (batch 2), and directly compare Scout to widely used XL-MS search engines (batches 3 and 4).

INSTRUMENT(S): Orbitrap Fusion Lumos

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Max Ruwolt  

LAB HEAD: Fan Liu

PROVIDER: PXD052022 | Pride | 2024-08-03

REPOSITORIES: Pride

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Dataset's files

Source:
Action DRS
264_plus_300_plus_1460human.fasta Fasta
264_plus_300human.fasta Fasta
26S_proteasome_yeast.fasta Fasta
4000_random_mito_plus_Ecoli_entrapment.fasta Fasta
540_plus_3460human.fasta Fasta
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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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