PXD027234

PXD027234 is an original dataset announced via ProteomeXchange.

Title	Cross-linking/Mass Spectrometry Combined with Ion Mobility on a timsTOF Pro Instrument for Structural Proteomics
Description	The combination of cross-linking/mass spectrometry (XL-MS) and ion mobility is still underexplored for conducting protein conformational and protein-protein interaction studies. We present a method for analyzing cross-linking mixtures on a timsTOF Pro mass spectrometer that allows separating ions based on their gas phase mobilities. Cross-linking was performed with three urea-based MS-cleavable cross-linkers that deliver distinct fragmentation patterns for cross-linked species upon collisional activation. The discrimination of cross-linked species from non-cross-linked peptides was readily performed based on their collisional cross sections. We demonstrate the general feasibility of our combined XL-MS/ion mobility approach for three protein systems of increasing complexity: (i) Bovine serum albumin, (ii) E. coli ribosome, and (iii) HEK293T cell nuclear extracts. We identified a total of 623 unique cross-linking sites for BSA, 670 for the E. coli ribosome, and 1,617 unique cross-links for nuclear extracts, corresponding to 1,088 intra- and 529 interprotein interactions and yielding 564 distinct protein-protein interactions. Our results underline the strength of combining XL-MS with ion mobility not only for deriving 3D-structures of single proteins, but also for performing system-wide protein interaction studies.
HostingRepository	PRIDE
AnnounceDate	2022-03-17
AnnouncementXML	Submission_2022-03-17_02:51:00.032.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Christian Ihling
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562; scientific name: Bos taurus (Bovine); NCBI TaxID: 9913; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	iodoacetamide derivatized residue
Instrument	timsTOF Pro

Revision	Datetime	Status	ChangeLog Entry
0	2021-07-12 01:42:41	ID requested
⏵ 1	2022-03-17 02:51:00	announced

Ihling CH, Piersimoni L, Kipping M, Sinz A, Cross-Linking/Mass Spectrometry Combined with Ion Mobility on a timsTOF Pro Instrument for Structural Proteomics. Anal Chem, 93(33):11442-11450(2021) [pubmed]

submitter keyword: Chemical Cross-Linking, Ion Mobility, Mass Spectrometry, Protein 3D-Structure, Protein Interaction Networks

Andrea Sinz
contact affiliation	Department of Pharmaceutical Chemistry & Bioanalytics Center for Structural Mass Spectrometry Institute of Pharmacy Martin Luther University Halle-Wittenberg Kurt-Mothes-Str. 3, Entrance C D-06120 Halle/Saale
contact email	andrea.sinz@pharmazie.uni-halle.de
lab head
Christian Ihling
contact affiliation	MLU Halle, Inst. f. Pharmacy
contact email	christian.ihling@pharmazie.uni-halle.de
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD027234
     1. Label: PRIDE project
     2. Name: Cross-linking/Mass Spectrometry Combined with Ion Mobility on a timsTOF Pro Instrument for Structural Proteomics