PXD029252

PXD029252 is an original dataset announced via ProteomeXchange.

Title	Mimicked synthetic ribosomal protein complex for benchmarking cross-linking mass spectrometry workflows
Description	The field of cross-linking mass spectrometry has matured to a frequently used tool for the investiga-tion of protein structures as well as interactome studies up to a system wide level. The growing com-munity generated a broad spectrum of applications, linker types, acquisition strategies and specialized data analysis tools, which makes it challenging, especially for newcomers, to decide for an appropriate analysis workflow. Therefore, we here present a large and flexible synthetic peptide library as reliable instrument to benchmark cross-linkers with different reactive sites as well as acquisition techniques and data analysis algorithms. Additionally, we provide a tool, IMP-X-FDR, that calculates the real FDR, compares results across search engine platforms and analyses crosslink properties in an auto-mated manner. The library was used with the reagents DSSO, DSBU, CDI, ADH, DHSO and azide-a-DSBSO and data were analysed using the algorithms MeroX, MS Annika, XlinkX, pLink and Max-Lynx. We thereby show that the correct algorithm and search setting choice is highly important to im-prove ID rate and FDR in combination with software and sample-complexity specific score cut-offs. When analysing DSSO data with MS Annika, we reach high identification rates of up to ~70 % of the theoretical maximum (i.e. 700 unique lysine-lysine cross-links) while maintaining a low real FDR of < 3 % at cross-link level and with extraordinary high reproducibility, representatively showing that our test system delivers valuable and statistically solid results.
HostingRepository	PRIDE
AnnounceDate	2024-04-04
AnnouncementXML	Submission_2024-04-03_16:58:02.449.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Manuel Matzinger
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562;
ModificationList	monohydroxylated residue
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2021-10-20 08:13:23	ID requested
1	2022-05-24 08:06:14	announced
2	2023-05-14 14:58:17	announced	2023-05-14: Updated project metadata.
3	2023-05-14 15:01:37	announced	2023-05-14: Updated project metadata.
4	2023-05-14 15:03:01	announced	2023-05-14: Updated project metadata.
⏵ 5	2024-04-03 16:58:03	announced	2024-04-04: Updated project metadata.

Matzinger M, Vasiu A, Madalinski M, M, ü, ller F, Stanek F, Mechtler K, Mimicked synthetic ribosomal protein complex for benchmarking crosslinking mass spectrometry workflows. Nat Commun, 13(1):3975(2022) [pubmed]

10.1038/s41467-022-31701-w;

ProteomeXchange project tag: EPIC-XS

submitter keyword: mass spectrometry, ribosome, FDR,crosslinking

Karl Mechtler
contact affiliation	Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
contact email	karl.mechtler@imp.ac.at
lab head
Manuel Matzinger
contact affiliation	IMP / University of Vienna
contact email	manuel.matzinger@imp.ac.at
dataset submitter

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://ftp.pride.ebi.ac.uk/pride/data/archive/2022/05/PXD029252

PRIDE project URI

• PRIDE
  1. PXD029252
     1. Label: PRIDE project
     2. Name: Mimicked synthetic ribosomal protein complex for benchmarking cross-linking mass spectrometry workflows