PXD008348

PXD008348 is an original dataset announced via ProteomeXchange.

Title	Comprehensive identification of crosslinked peptides from methyltransferase Hmt1 and its substrate Npl3: use of multiple crosslinkers, mass spectrometry approaches and software platforms
Description	Chemical-Crosslinking Mass Spectrometry (XLMS) using MS-cleavable crosslinkers is fast becoming an established technique in the study of protein-protein interactions for both small and large scale samples. With the increased uptake of XLMS as a technique, different combinations of crosslinker types, fragmentation strategies and analysis programs are being applied to a diverse array of biological samples. This study is focused on understanding how the three variables of an XLMS experiment – crosslinker type, fragmentation and program – could generate differences in identifications, leading to increased biological coverage of a sample. Here we probe for the first time, the known enzyme:substrate interaction between yeast arginine methyltransferase Hmt1p and its substrate, heterologous nucleolar protein Npl3p. We use this known interaction as a platform to compare two analysis programs, MeroX and XlinkX2.0, using two crosslinker types, DSSO and DSBU, and two mass-spectrometry fragmentation strategies, CID/ETD and SteppedHCD. Through these we also compare different algorithm strategies, Precursor and Reporter-Ion, as well as assess the impact of restricting data searches to lysine only crosslinks versus the inclusion of serine, threonine and tyrosine as reactive residues. From this analysis we show direct evidence of Hmt1p in contact with its known methylation sites on Npl3p, the intrinsically disordered “SRGG” region. We also show through our multi-crosslinker, multi-fragmentation and multi-software approach that two approaches leads to greater understanding and depth of a crosslinked sample, and this is due to some combinations of experimental variables creating greater coverage of crosslinks than others.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:42:31.016.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Daniela-Lee Smith
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562; scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationList	monomethylated residue; monohydroxylated residue; dimethylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos; Q Exactive Plus

Revision	Datetime	Status	ChangeLog Entry
0	2017-12-01 08:02:09	ID requested
1	2018-07-20 02:05:21	announced
⏵ 2	2024-10-22 04:42:39	announced	2024-10-22: Updated project metadata.

10.1021/acs.analchem.8b01525;

Smith DL, G, ö, tze M, Bartolec TK, Hart-Smith G, Wilkins MR, Characterization of the Interaction between Arginine Methyltransferase Hmt1 and Its Substrate Npl3: Use of Multiple Cross-Linkers, Mass Spectrometric Approaches, and Software Platforms. Anal Chem, 90(15):9101-9108(2018) [pubmed]

curator keyword: Biological

submitter keyword: Crosslinking-Mass Spectrometry, MS-Cleavable linkers

Marc R Wilkins
contact affiliation	Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, UNSW Sydney, NSW 2052, Australia
contact email	m.wilkins@unsw.edu.au
lab head
Daniela-Lee Smith
contact affiliation	University of New South Wales
contact email	daniela-lee.smith@unsw.edu.au
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/2018/07/PXD008348

PRIDE project URI

• PRIDE
  1. PXD008348
     1. Label: PRIDE project
     2. Name: Comprehensive identification of crosslinked peptides from methyltransferase Hmt1 and its substrate Npl3: use of multiple crosslinkers, mass spectrometry approaches and software platforms