PXD008348 is an
original dataset announced via ProteomeXchange.
Dataset Summary
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 |
Dataset History
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. |
Publication List
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] |
Keyword List
curator keyword: Biological |
submitter keyword: Crosslinking-Mass Spectrometry, MS-Cleavable linkers |
Contact List
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 | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD008348
- Label: PRIDE project
- Name: Comprehensive identification of crosslinked peptides from methyltransferase Hmt1 and its substrate Npl3: use of multiple crosslinkers, mass spectrometry approaches and software platforms