Dataset Information

TAILS on mouse skin deficient for ADAMTS2 and ADAMTS14

ABSTRACT: TAILS 4-Plex on mouse skin. 114 - WT; 115 - ADAMTS2-KO; 116 - ADAMTS14-KO; 117 - ADAMTS2TS14-double KO.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Mus Musculus (mouse)

TISSUE(S): Skin

DISEASE(S): Ehlers-danlos Syndrome Dermatosparaxis Type

SUBMITTER: Mourad Bekhouche

LAB HEAD: Alain Colige

PROVIDER: PXD022179 | Pride | 2021-04-16

REPOSITORIES: pride

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Publications

In vivo N-Terminomics Highlights Novel Functions of ADAMTS2 and ADAMTS14 in Skin Collagen Matrix Building.

Leduc Cédric C Dupont Laura L Joannes Loïc L Monseur Christine C Baiwir Dominique D Mazzucchelli Gabriel G Deroanne Christophe C Colige Alain A Bekhouche Mourad M

Frontiers in molecular biosciences 20210319

A disintegrin and metalloproteinase with thrombospondin type I motif (ADAMTS)2 and ADAMTS14 were originally known for their ability to cleave the aminopropeptides of fibrillar collagens. Previous work using N-terminomic approach (N-TAILS) in vitro led to the identification of new substrates, including some molecules involved in TGF-β signaling. Here, N-TAILS was used to investigate the substrates of these two enzymes in vivo, by comparing the N-terminomes of the skin of wild type m ...[more]

PMID: 33816558

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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.

Project description:Part I - SI-NET tumors High Resolution Isoelectric Focusing (HiRIEF) LC-MS and relative quantification by iTRAQ 8-plex was used to analyze 14 small intestinal neuroendocrine tumors (SI-NETs). The data was obtained from two separate TMT10plex sets and linked by a single internal pooled standard. The internal pooled standard was made by combining equal aliquots of the tryptic peptide mixtures from each of the 14 tissue samples. iTRAQ set1 was composed of 7 SI-NET samples, all from different individuals, and internal pooled standard labelled as follows: Channel 113 (sample Screen-1 with liver metastasis), Channel 114 (sample Screen-8 with liver metastasis), Channel 115 (sample Screen-3 with liver metastasis), Channel 116 (sample Screen-2 with liver metastasis), Channel 117 (sample Screen-5 no liver metastasis), Channel 118 (sample Screen-4 no liver metastasis), Channel 119 (sample Screen-10 no liver metastasis), Channel 121 (internal pooled standard). iTRAQ set2 was composed of 7 SI-NET samples, all from different individuals, and internal pooled standard labelled as follows: Channel 113 (sample Screen-7 with liver metastasis), Channel 114 (sample Screen-11 with liver metastasis), Channel 115 (sample Screen-13 with liver metastasis), Channel 116 (sample Screen-6 no liver metastasis), Channel 117 (sample Screen-12 no liver metastasis), Channel 118 (sample Screen-9 no liver metastasis), Channel 119 (sample Screen-14 no liver metastasis), Channel 121 (internal pooled standard). Part II - time course profiling in cell lines High Resolution Isoelectric Focusing (HiRIEF) LC-MS and relative quantification by TMT 10-plex was used to analyze cellular response to the neddylation inhibitor pevonedistat (MLN4924) at different timepoints in two SI-NET (small intestinal neuroendocrine tumors) cell lines. The data was obtained from two separate TMT 10-plex experiments. TMT set1 includes a time course experiment upon pevonedistat treatment of CNDT2 cells with harvests at 2h, 6h, 12h and 24h after treatment as well as of untreated control cells. Isobaric tag labelling of peptide samples with TMT10plex was used as follows. Biological duplicate controls (TMT channels 126, 127N), duplicate 2h (127C, 128N), duplicate 6h (128C, 129N), duplicate 12h (129C, 130N) and duplicate 24h (130C, 131) samples were employed. TMT set2 includes a time course experiment upon pevonedistat treatment of HC45 cells with harvests at 2h, 6h, 12h and 24h after treatment as well as of untreated control cells. Isobaric tag labelling of peptide samples with TMT10plex was used as follows. Biological duplicate controls (TMT channels 126, 127N), duplicate 2h (127C, 128N), duplicate 6h (128C, 129N), duplicate 12h (129C, 130N) and duplicate 24h (130C, 131) samples were employed.

			Action	DRS
	CLIPPER_ExpA_L1-L3.xls	Xls
	CLIPPER_ExpA_L1-L4.xls	Xls
	CLIPPER_ExpB_L1-L2.xls	Xls
	CLIPPER_ExpB_L1-L3.xls	Xls
	CLIPPER_ExpB_L1-L4.xls	Xls

Dataset Information

TAILS on mouse skin deficient for ADAMTS2 and ADAMTS14

Dataset's files

Publications

<i>In vivo</i> N-Terminomics Highlights Novel Functions of ADAMTS2 and ADAMTS14 in Skin Collagen Matrix Building.

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