Dataset Information

Time-resolved analysis of the matrix metalloproteinase 10 substrate degradome.

ABSTRACT: Proteolysis is an irreversible post-translational modification that affects intra- and intercellular communication by modulating the activity of bioactive mediators. Key to understanding protease function is the system-wide identification of cleavage events and their dynamics in physiological contexts. Despite recent advances in mass spectrometry-based proteomics for high-throughput substrate screening, current approaches suffer from high false positive rates and only capture single states of protease activity. Here, we present a workflow based on multiplexed terminal amine isotopic labeling of substrates for time-resolved substrate degradomics in complex proteomes. This approach significantly enhances confidence in substrate identification and categorizes cleavage events by specificity and structural accessibility of the cleavage site. We demonstrate concomitant quantification of cleavage site spanning peptides and neo-N and/or neo-C termini to estimate relative ratios of noncleaved and cleaved forms of substrate proteins. By applying this strategy to dissect the matrix metalloproteinase 10 (MMP10) substrate degradome in fibroblast secretomes, we identified the extracellular matrix protein ADAMTS-like protein 1 (ADAMTSL1) as a direct MMP10 substrate and revealed MMP10-dependent ectodomain shedding of platelet-derived growth factor receptor alpha (PDGFR?) as well as sequential processing of type I collagen. The data have been deposited to the ProteomeXchange Consortium with identifier PXD000503.

SUBMITTER: Schlage P

PROVIDER: S-EPMC3916655 | biostudies-literature | 2014 Feb

REPOSITORIES: biostudies-literature

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Time-resolved analysis of the matrix metalloproteinase 10 substrate degradome.

Schlage Pascal P Egli Fabian E FE Nanni Paolo P Wang Lauren W LW Kizhakkedathu Jayachandran N JN Apte Suneel S SS auf dem Keller Ulrich U

Molecular & cellular proteomics : MCP 20131126 2

Proteolysis is an irreversible post-translational modification that affects intra- and intercellular communication by modulating the activity of bioactive mediators. Key to understanding protease function is the system-wide identification of cleavage events and their dynamics in physiological contexts. Despite recent advances in mass spectrometry-based proteomics for high-throughput substrate screening, current approaches suffer from high false positive rates and only capture single states of pr ...[more]

PMID: 24281761

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Project description:20110318_GluC: Cell culture supernatants from Balb/c 3T3 mouse fibroblasts that had been incubated with the endoproteinase GluC (Staphylococcus aureus protease V8) as test protease for 1, 2, 4, 8, and 16 hours or buffer alone (0, 12, and 16 hours controls) were subjected to 8plex-iTRAQ-TAILS analysis. Labeling scheme: 113: 0h control, 114: 1h, 115: 2h, 116: 4h, 117: 8h, 118: 12h control, 119: 16h, 121: 16h control. 20130214_MMP10: Cell culture supernatants from matrix metalloproteinase (MMP) 10 deficient murine embryonic fibroblasts that had been incubated with recombinant human MMP10 as test protease for 1, 2, 4, 8, and 16 hours or buffer alone (0 and 16 hours controls) were subjected to 8plex-iTRAQ-TAILS analysis. Labeling scheme: 113: 0h control, 114: 1h, 115: 2h, 116: 4h, 117: 8h, 118: 12h, 119: 16h, 121: 16h control.MS data analysis: Mascot Distiller (Matrix Science) was used to extract peak lists from raw files and for merging of corresponding CID/HCD spectra pairs. Peak lists (mgf) were searched by Mascot v2.3 search engine against a mouse UniProtKB database (release 2012_03; 54232 entries), to which reversed decoy sequences as well as sequences for common contaminants and either for GluC or for human MMP10, respectively, had been added and with following parameters: semi-Arg-C for enzyme specificity allowing up to 2 missed cleavages; carbamidomethyl(C), iTRAQ(K) as fixed modifications; acetyl (N-term), iTRAQ(N-term), oxidation(M), and deamidation(NQ) as variable modifications; parent mass error at 10 ppm, fragment mass error at 0.8 Da. For GluC experiments an additional search was performed using the same parameters but with semi-GluC as enzyme and allowing up to 5 missed cleavages. The Trans-Proteomic Pipeline (TPP v4.6, rev 1, Build 201212051643)46 was used to secondary validate Mascot search results and to compile a single peptide list from all peptide fractions obtained from both the pre-pullout and the pullout samples. First, data were processed by PeptideProphet setting the ‘minimum peptide length’ to 1, using ‘accurate mass binning’ and omitting the ‘NTT model’. Next, iProphet was employed for additional validation and for combining PeptideProphet results from multiple searches, and only peptides with an iProphet probability of >=0.9 (corresponding to false discovery rate (decoy) of <1%) were included in subsequent analyses. For relative quantification iTRAQ reporter ion intensities were extracted from mgf files using a modified version of i-Tracker47 with a mass tolerance of 0.1 Da and purity corrections supplied by the iTRAQ manufacturer and assigned to filtered peptides.

Dataset Information

Time-resolved analysis of the matrix metalloproteinase 10 substrate degradome.

Publications

Time-resolved analysis of the matrix metalloproteinase 10 substrate degradome.

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