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CLIPPER: an add-on to the Trans-Proteomic Pipeline for the automated analysis of TAILS N-terminomics data
-
Ulrich auf dem Keller
and
Christopher M. Overall
Published/Copyright:
November 13, 2012
Abstract
Data analysis in proteomics is complex and with the extra challenges involved in the interpretation of data from N-terminomics experiments, this can be daunting. Therefore, we have devised a rational pipeline of steps to approach N-terminomics data analysis in a statistically-based and valid manner. We have automated these steps in CLIPPER, an add-on to the Trans-Proteomic Pipeline (TPP). Applying CLIPPER to the analysis of N-terminomics data generated by terminal amine isotopic labeling of substrates (TAILS) enables high confidence peptide to protein assignment, protein N-terminal characterization and annotation, and for protease analysis readily allows protease substrate discovery with high confidence.
Keywords: degradomics; N-terminomics; protease; proteomics; terminal amine isotopic labeling of substrates (TAILS); Trans-Proteomic Pipeline (TPP)
Received: 2012-8-10
Accepted: 2012-9-11
Published Online: 2012-11-13
Published in Print: 2012-12-01
©2012 by Walter de Gruyter Berlin Boston
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Keywords for this article
degradomics;
N-terminomics;
protease;
proteomics;
terminal amine isotopic labeling of substrates (TAILS);
Trans-Proteomic Pipeline (TPP)
Articles in the same Issue
- Masthead
- Masthead
- Guest Editorial
- Highlight: 29th Winter School on Proteinases and Their Inhibitors
- Highlight: 29th Winter School on Proteinases and their Inhibitors
- Genetic polymorphisms in the human tissue kallikrein (KLK) locus and their implication in various malignant and non-malignant diseases
- Effects of cathepsin K deficiency on intercellular junction proteins, luminal mucus layers, and extracellular matrix constituents in the mouse colon
- Three-dimensional cultures modeling premalignant progression of human breast epithelial cells: role of cysteine cathepsins
- Cysteine cathepsins are not critical for TRAIL- and CD95-induced apoptosis in several human cancer cell lines
- Dissecting the impact of Frizzled receptors in Wnt/β-catenin signaling of human mesenchymal stem cells
- Overexpression of the urokinase receptor splice variant uPAR-del4/5 in breast cancer cells affects cell adhesion and invasion in a dose-dependent manner and modulates transcription of tumor-associated genes
- IGF-I receptor phosphorylation is impaired in cathepsin X-deficient prostate cancer cells
- Cell surface engineering of renal cell carcinoma with glycosylphosphatidylinositol-anchored TIMP-1 blocks TGF-β1 activation and reduces regulatory ID gene expression
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- Proteolysis
- Characterization of angiotensin I-converting enzyme N-domain selectivity using positional-scanning combinatorial libraries of fluorescence resonance energy transfer peptides
- Mast cells limit extracellular levels of IL-13 via a serglycin proteoglycan-serine protease axis
