Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

XL-MS data analysis with MeroX and XlinkX

ABSTRACT: Comparison of MeroX in different modes and XlinkX upon variation of database size based on DSBU linked BSA as test-dataset

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): Bos Taurus (bovine)

SUBMITTER: Manuel Matzinger

LAB HEAD: Karl Mechtler

PROVIDER: PXD021648 | Pride | 2020-11-17

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	BSA-10000prot-human.fasta	Fasta
	BSA-1000prot-human.fasta	Fasta
	BSA-100prot-human.fasta	Fasta
	BSA-10prot-human.fasta	Fasta
	BSA-only.fasta	Fasta

Items per page:

1 - 5 of 31

Publications

Cleavable Cross-Linkers and Mass Spectrometry for the Ultimate Task of Profiling Protein-Protein Interaction Networks <i>in Vivo</i>.

Matzinger Manuel M Mechtler Karl K

Journal of proteome research 20201105 1

Cross-linking mass spectrometry (XL-MS) has matured into a potent tool to identify protein-protein interactions or to uncover protein structures in living cells, tissues, or organelles. The unique ability to investigate the interplay of proteins within their native environment delivers valuable complementary information to other advanced structural biology techniques. This Review gives a comprehensive overview of the current possible applications as well as the remaining limitations of the techn ...[more]

PMID: 33151691

Similar Datasets

Comprehensive identification of crosslinked peptides from methyltransferase Hmt1 and its substrate Npl3: use of multiple crosslinkers, mass spectrometry approaches and software platforms

Project 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.

2018-07-20 | PXD008348 | Pride

Mimicked synthetic ribosomal protein complex for benchmarking cross-linking mass spectrometry workflows

Project 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.

2022-05-24 | PXD029252 | Pride

A Simple Cross-Linking/Mass Spectrometry Workflow to Study System-Wide Protein Interactions in Drosophila Embryos

Project description:We provide a cross-linking/MS workflow that can be applied to complex systems. The software tool MeroX 2.0 can be used to identify cross-linked peptide on a proteome-wide level. We applied the workflow to extracts of Drosophila embryos and identified 5,129 unique cross-linked residue pairs in biological triplicates.

2019-07-09 | PXD012546 | Pride

2) Twisting Urea- to Imide-Based Mass Spectrometry-Cleavable Cross-Linkers to Embed Affinity Tags

Project description:Disuccinimidyl dibutyric urea (DSBU) is a mass spectrometry (MS)-cleavable cross-linker that has been applied to multiple applications in structural biology, ranging from isolated protein complexes to comprehensive system-wide interactomics. DSBU facilitates a rapid and reliable identification of cross-links through the dissociation of its urea group in the gas-phase. In this study, we further advance the structural capabilities of DSBU by twisting the urea group into an imide, thus introducing a novel class of cross-linkers. This modification preserves the MS-cleavability of the amide bond, granted by the two acyl groups of the imide function. The central nitrogen atom enables the introduction of affinity purification tags. Here, we introduce disuccinimidyl dibutyric imide (DSBI) as prototype of this class of cross-linkers. It features a phosphonate handle for immobilized metal ion affinity chromatography (IMAC) enrichment. We detail DSBI synthesis and describe its behavior in solution and in the gas-phase while cross-linking isolated proteins and human cell lysates. DSBI and DSBU cross-links are compared at the same enrichment depths to bridge these two cross-linker classes. We validate DSBI cross-links by mapping them in high-resolution structures of large protein assemblies . The cross-links observed yield insights into the morphology of intrinsically disordered proteins (IDPs) and their complexes. The DSBI linker might spearhead a novel class of MS-cleavable and enrichable cross-linkers

2024-09-03 | PXD050960 | Pride

XL-MS data of BAM and SurA binding

Project description:We present XL-MS data of the BAM:SurA complex to define the interaction sites for SurA on BAM

2022-07-12 | PXD030209 | Pride

A synthetic crosslinked peptide library for benchmarking crosslinking mass spectrometry search engines

Project description:We have created a synthetic crosslinked peptide library to benchmark crosslinking mass spectrometry search engines. The unique benefit of the library is knowing which identified crosslinks are true and which are false. The data collected from mass spectrometry measurements of the peptide library were used to assess the most frequently used search algorithms. The datasets included will provide an important resource for the crosslinking community to evaluate and optimise search engines, results from which have far-reaching implications.

2020-07-28 | PXD014337 | Pride

XL-MS data of trigger factor and GAPDH binding

Project description:We present XL-MS data of the trigger factor:GAPDH complex to define the interaction sites for GAPDH on trigger factor.

2022-06-07 | PXD029365 | Pride

The molecular bases of spinal muscular atrophy

Project description:Spinal muscular atrophy (SMA) is a neurodegenerative disease caused by the absence of a functional Survival of Motor Neuron 1 gene (SMN1). The nearly identical paralog, SMN2, cannot compensate for the loss of SMN1 because exon 7 is aberrantly skipped from most SMN2 transcripts, a process mediated by synergistic activities of Sam68/KHDR1 and hnRNP A1. This results in the production of a truncated, non-functional protein that is rapidly degraded. Here we present several crystal structures of Sam68 RNA-binding domain (RBD). Sam68-RBD forms stable symmetric homodimers by antiparallel association of helices α3 from two monomers. However, the details of domain organization and the dimerization interface differ significantly from previously characterized homologs. We demonstrate that Sam68 and hnRNP A1 bind proximal but distinct motifs within the central region of SMN2(ex7). Our findings have important implications for the etiology of SMA and open new avenues for the design of novel therapeutics to treat splicing diseases.

2024-05-23 | PXD033055 | Pride

Reanalysis of a proteome-wide level study with MaxLynx

Project description:Reanalysis of the publicly available proteome-wide level dataset with DSBU from Goetze et al., Anal Chem. 2019 (PXD012546).

2022-01-11 | PXD027188 | Pride

In vivo and in vitro characterization and structural analysis of human DPCD protein in complex with RUVBL1/RUVBL2 AAA-ATPases

Project description:DPCD is a protein that may play a role in cilia formation and whose absence leads to primary ciliary dyskinesia (PCD), a rare disease caused by impairment of ciliated cells. Except for high-throughput studies that identified DPCD as a possible RUVBL1 (R1) and RUVBL2 (R2) partner, no in-depth cellular, biochemical, and structural investigations involving DPCD have been reported so far. R1 and R2 proteins are ubiquitous highly conserved AAA+ family ATPases that assemble and mature a plethora of macromolecular complexes and are pivotal in numerous cellular processes, especially by guaranteeing a co-chaperoning function within R2TP or R2TP-like machineries. In the present study, we identified DPCD as a new R1R2 partner in vivo. We show that DPCD interacts directly with R1 and R2 in vitro and in cells. We characterized the physico-chemical properties of DPCD in solution and built 3D structural models of DPCD alone and in complex with R1R2 validated by experimental data combining Small-Angle X-ray Scattering and Cross-linking Mass Spectrometry, among others. Interestingly, DPCD disrupts the dodecameric state of R1R2 complex upon binding and this interaction occurs mainly via the DII domains of R1R2.

2023-04-06 | PXD031339 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data