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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

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			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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Proteome-scale recombinant standard datasets for XL-MS

Project description: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.

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2020-03-26 | PXD016554 | Pride

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