Name: A quantitative proteomics design for systematic identification of protease cleavage events.
Keywords: Not available

OmicsDI

Browse
Submit Data
Databases
API
Help

Dataset Information

249 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A quantitative proteomics design for systematic identification of protease cleavage events.

ABSTRACT: Recombinant mouse cathepsin D was added to lysates of mouse dendritic cells. Neo-N-terminal peptides were isolated by N-terminal COFRADIC and their presence in ratios distributed distinct from other peptides was induced by mixing light and heavy labeled proteins according to a novel quantitative design.

INSTRUMENT(S): LTQ Orbitrap, instrument model

ORGANISM(S): Homo Sapiens (human) Mus Musculus (mouse)

SUBMITTER: Francis Impens

PROVIDER: PRD000281 | Pride | 2010-08-03

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Similar Datasets

TAILS proteomics of murine pancreatic tumors

Project description:Aberrant proteolysis by cysteine cathepsins is implicated in carcinogenesis, but knowledge of cathepsin substrates mediating tumor-promoting or suppressing effects is limited. Here we characterize tumor proteome and in vivo cathepsin substrates using cathepsin knockout mice and the RIP1-Tag2 model of pancreatic islet carcinogenesis. Applying an unbiased systems-level proteomics approach, Terminal Amine Isotopic Labeling of Substrates (TAILS), we identified cysteine cathepsin B, H, L, S, Z substrates and their cleavage sites. Among 1,935 proteins and 1,114 N-termini identified by TAILS using 8-plex iTRAQ protein labeling, 145 neo-N-termini were significantly changed in one (55%) or more knockouts suggesting a lack of direct compensation at substrate level by other cathepsins. Most affected N-termini (56-83% for different cathepsins) represented degradative cathepsin activity, whereas 17-44% of neo-N termini represented stable proteolytic products in the tumors and were enriched for extracellular proteins. We identified candidate substrates for mediating signaling roles of cysteine cathepsins in tumorigenesis.

2016-08-08 | PXD003637 | Pride

A quantitative proteomics design for systematic identification of protease cleavage events.

Project description: Not available

| S-EPMC2953924 | biostudies-literature

HIV-1 protease degradomics - Identify proteins cleaved during HIV-1 infection in an unbiased manner and on a proteome-wide scale

Project description:To identify proteins cleaved during HIV-1 infection in an unbiased manner and on a proteome-wide scale, positional proteomics was used to identify proteolysis-reporter peptides or so-called neo-N-terminal peptides. The spectra stored in this PRIDE experiment (n=148) are the highest scoring spectra of neo-N-terminal peptides generated by cleavage of recombinant HIV-1 protease added to a lysate of human Jurkat T-cells.

2012-08-07 | PRD000378 | Pride

In vitro characterization of caspase-3 cleavage sites by LATE and HYATNE

Project description:Proteins' N-termini contain information about their biochemical properties and functions, and they can undergo co- or post-translational modifications, as well as be processed by proteases. To expand the coverage of the N-terminome, we have developed LATE (LysN Amino Terminal Enrichment), a method that uses selective chemical derivatization of α-amines to isolate the N-terminal peptides. We applied LATE in combination with other N-terminomic method to study caspase-3 mediated proteolysis both in vitro and during apoptosis in cells. This enable us to identify many unreported caspase-3 cleavages, including some that cannot be identified by other methods. Furthermore, we find direct evidence that some of the caspase-3 generated neo-N-termini can be further modified by Nt-acetylation. This provides a global picture of the caspase-3 degradome and uncovers previously unrecognised functional crosstalk between post-translational Nt-acetylation and caspase proteolysis pathways.

2023-06-27 | PXD036593 | Pride

Cell-based characterization of caspase-3 cleavage sites by LATE and HYATNE

2023-06-27 | PXD036648 | Pride

proteome profiling - Switching off IMMP2L signaling drives senescence via simultaneous metabolic alteration and blockage of cell death

Project description:quantification proteomics and neo-N-terminal peptides enrichment

2018-06-06 | PXD006602 | Pride

In situ synthesis of peptide microarrays - shadow mask design [1]

Project description:A computer program was used to create random amino acid sequences based on and restricted by physical shadow masks which will be used for lithography-based synthesis of peptides. The output from this algorithm was used to create peptides that were synthesized by Sigma Aldrich, and printed onto glass slides. The arrays contained 384 peptides printed in duplicate for each of 4 different mask designs. 52 different monoclonal antibodies were incubated on these microarrays and analyzed for their propensity to bind the peptides created from each mask set. The diversity of binding served as a proxy for the 'randomness' of these peptides, and provided information about how many masks are needed to truly generate random sequence peptides.

2014-01-16 | GSE49217 | GEO

Cleavage of the pseudoprotease iRhom2 by the signal peptidase complex reveals an ER-to-nucleus signalling pathway

Project description:iRhoms are pseudoprotease members of the rhomboid-like superfamily and are cardinal regulators of inflammatory and growth factor signaling; they function primarily by recognizing transmembrane domains of their clients. Here, we report a mechanistically distinct nuclear function of iRhoms, showing that both human and mouse iRhom2 are non-canonical substrates of signal peptidase complex (SPC), the protease that removes signal peptides from secreted proteins. Cleavage of iRhom2 generates an N-terminal fragment that enters the nucleus and modifies the transcriptome, in part by binding C-terminal binding proteins (CtBPs). The biological significance of nuclear iRhom2 is indicated by elevated levels in skin biopsies of patients with psoriasis, tylosis with oesophageal cancer (TOC), and non-epidermolytic palmoplantar keratoderma (NEPPK); increased iRhom2 cleavage in a keratinocyte model of psoriasis; and nuclear iRhom2 promoting proliferation of keratinocytes. Overall, this work identifies an unexpected SPC-dependent ER-to-nucleus signaling pathway and demonstrates that iRhoms can mediate nuclear signaling.

2024-01-04 | GSE219008 | GEO

In situ synthesis of peptide microarrays - shadow mask design [1]

2014-01-16 | E-GEOD-49217 | biostudies-arrayexpress

Intestinal Differentiation Involves Cleavage of Histone H3 NTerminal Tails by Multiple Proteases

Project description:The proteolytic cleavage of histone tails, also termed histone clipping, has been described as a mechanism for permanent removal of post-translational modifications (PTMs) from histone proteins. Such activity has been ascribed to ensure regulatory function in key cellular processes such as differentiation, senescence and transcriptional control for which different histone-specific proteases has been described. However, all these studies were exclusively performed using cell lines cultured in vitro and no clear evidences that histone clipping is regulated in vivo has been reported. Here we show that histone H3 N-terminal tails undergo extensive cleavage in the differentiated cells of the villi fraction of the mouse intestinal epithelium. Combining biochemical methods, 3D organoids cultures and in vivo approaches, we demonstrate that intestinal H3 clipping is the result of multiple proteolytic activities. We identified Trypsins and Cathepsin L as specific H3 tail proteases active in small intestinal differentiated cells and showed that their proteolytic activity is differentially affected by the PTM pattern of histone H3 tails. Together, our findings provide in vivo evidences of H3 tail proteolysis in mammalian tissues directly linking H3 clipping to cell differentiation.

2020-12-04 | GSE160776 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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