CLIPPER: an add-on to the Trans-Proteomic Pipeline for the automated analysis of TAILS N-terminomics data

No abstract is available for this paper.

• Publication year

  2012

• Venue

  Biological chemistry

• Publication date

  2012-12-01

• Fields of study

  Biology, Medicine, Chemistry, Computer Science

• Identifiers
  DOI 10.1515/hsz-2012-0269PMID 23667905
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• R: A language and environment for statistical computing.

  2014cited by this paper
• N-terminal acetylation and other functions of Nα-acetyltransferases

  2012cited by this paper
• Biochemical Characterization and N-terminomics Analysis of Leukolysin, the Membrane-type 6 Matrix Metalloprotease (MMP25)

  2012cited by this paper
• N- and C-terminal degradomics: new approaches to reveal biological roles for plant proteases from substrate identification.

  2012cited by this paper
• The substrate degradome of meprin metalloproteases reveals an unexpected proteolytic link between meprin β and ADAM10

  2012cited by this paper
• TopFIND 2.0—linking protein termini with proteolytic processing and modifications altering protein function

  2011cited by this paper
• Factor Xa subsite mapping by proteome-derived peptide libraries improved using WebPICS, a resource for proteomic identification of cleavage sites

  2011cited by this paper
• TopFIND, a knowledgebase linking protein termini with function

  2011cited by this paper
• iProphet: Multi-level Integrative Analysis of Shotgun Proteomic Data Improves Peptide and Protein Identification Rates and Error Estimates*

  2011cited by this paper
• UniProt Knowledgebase: a hub of integrated protein data

  2011cited by this paper
• Proteomic Analyses Reveal an Acidic Prime Side Specificity for the Astacin Metalloprotease Family Reflected by Physiological Substrates

  2011cited by this paper
• Identifying and quantifying proteolytic events and the natural N terminome by terminal amine isotopic labeling of substrates

  2011cited by this paper
• Metalloprotease Meprin β Generates Nontoxic N-terminal Amyloid Precursor Protein Fragments in Vivo*

  2011cited by this paper
• A Statistics-based Platform for Quantitative N-terminome Analysis and Identification of Protease Cleavage Products

  2010cited by this paper
• Isotopic labeling of terminal amines in complex samples identifies protein N-termini and protease cleavage products

  2010cited by this paper
• Multiplex N-terminome Analysis of MMP-2 and MMP-9 Substrate Degradomes by iTRAQ-TAILS Quantitative Proteomics*

  2010cited by this paper
• Proteomic techniques and activity-based probes for the system-wide study of proteolysis.

  2010cited by this paper
• MS‐driven protease substrate degradomics

  2010influential reference
• Methods for combining peptide intensities to estimate relative protein abundance

  2010cited by this paper
• A guided tour of the Trans‐Proteomic Pipeline

  2010cited by this paper
• The Proteomics Identifications database: 2010 update

  2009cited by this paper
• Cell-based identification of natural substrates and cleavage sites for extracellular proteases by SILAC proteomics.

  2009cited by this paper
• Proteases: Multifunctional Enzymes in Life and Disease*

  2008cited by this paper
• In search of partners: linking extracellular proteases to substrates

  2007cited by this paper
• Reporting Protein Identification Data

  2006cited by this paper
• A statistical model for identifying proteins by tandem mass spectrometry.

  2003cited by this paper
• Modern applied statistics with S, 4th Edition

  2002cited by this paper
• Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search.

  2002cited by this paper
• Protease degradomics: A new challenge for proteomics

  2002cited by this paper
• The Bioperl toolkit: Perl modules for the life sciences.

  2002cited by this paper

• DICED (Database of Identified Cleavage Sites Endemic to Diseases States): A Searchable Web Interface for Terminomics/Degradomics

  2025cites this paper
• Data Processing and Analysis in Positional Proteomics

  2025influential citation
• Combined genetic-pharmacologic inactivation of tightly linked ADAMTS proteases in temporally specific windows uncovers distinct roles for versican proteolysis and glypican-6 in cardiac development

  2024cites this paper
• Comprehensive Overview of Bottom-Up Proteomics Using Mass Spectrometry

  2024cites this paper
• Comprehensive Overview of Bottom-Up Proteomics using Mass Spectrometry

  2023cites this paper
• CLIPPER 2.0: Peptide-Level Annotation and Data Analysis for Positional Proteomics

  2023cites this paper
• “Omics” approaches to determine protease degradomes in complex biological matrices

  2022cites this paper
• In vivo N-Terminomics Highlights Novel Functions of ADAMTS2 and ADAMTS14 in Skin Collagen Matrix Building

  2021cites this paper
• MANTI: Automated Annotation of Protein N-Termini for Rapid Interpretation of N-Terminome Data Sets

  2021cites this paper
• Mapping the N-Terminome in Tissue Biopsies by PCT-TAILS.

  2020cites this paper
• N-terminomics - its past and recent advancements.

  2020cites this paper
• Positional proteomics for identification of secreted proteoforms released by site-specific processing of membrane proteins.

  2019cites this paper
• Recent Technological Advances in the Mass Spectrometry-based Nanomedicine Studies: An Insight from Nanoproteomics.

  2019cites this paper
• Exploring Extracellular Matrix Degradomes by TMT-TAILS N-Terminomics.

  2019cites this paper
• Time-Resolved Analysis of Matrix Metalloproteinase Substrates in Complex Samples.

  2017cites this paper
• Multidimensional Analysis of Protease Substrates and Their Cellular Origins in Mixed Secretomes from Multiple Cell Types.

  2017cites this paper
• Profiling of Protein N-Termini and Their Modifications in Complex Samples.

  2017cites this paper
• Protein Terminal Profiling

  2017cites this paper
• Body Fluid Degradomics and Characterization of Basic N-Terminome.

  2017cites this paper
• Large-Scale Quantitative Proteomics Identifies the Ubiquitin Ligase Nedd4-1 as an Essential Regulator of Liver Regeneration.

  2017cites this paper
• Proteolytic Cleavage-Mechanisms, Function, and "Omic" Approaches for a Near-Ubiquitous Posttranslational Modification.

  2017cites this paper
• TAILS N-Terminomics and Proteomics Show Protein Degradation Dominates over Proteolytic Processing by Cathepsins in Pancreatic Tumors.

  2016cites this paper
• Quantitative proteomics and terminomics to elucidate the role of ubiquitination and proteolysis in adaptive immunity

  2016cites this paper
• Determination of the substrate repertoire of ADAMTS2, 3, and 14 significantly broadens their functions and identifies extracellular matrix organization and TGF‐β signaling as primary targets

  2016cites this paper
• Matrix Metalloproteinase Degradomics in Normal and Wounded Skin

  2015cites this paper
• Identification of Protease Substrates in Complex Proteomes by iTRAQ-TAILS on a Thermo Q Exactive Instrument

  2015cites this paper
• Proteomic approaches to uncover MMP function.

  2015cites this paper
• Matrix Metalloproteinase 10 Degradomics in Keratinocytes and Epidermal Tissue Identifies Bioactive Substrates With Pleiotropic Functions*

  2015cites this paper
• TAILS N-terminomic and proteomic datasets of healthy human dental pulp

  2015cites this paper
• Monitoring matrix metalloproteinase activity at the epidermal–dermal interface by SILAC‐iTRAQ‐TAILS

  2015cites this paper
• MMPs: From Genomics to Degradomics

  2015cites this paper
• A new transcriptional role for matrix metalloproteinase-12 in antiviral immunity

  2014cites this paper
• In Vivo Assessment of Protease Dynamics in Cutaneous Wound Healing by Degradomics Analysis of Porcine Wound Exudates*

  2014cites this paper
• In Vivo Assessment of Protease Dynamics in Cutaneous Wound Healing by Degradomics Analysis of Porcine Wound Exudates

  2014cites this paper
• Macrophage matrix metalloproteinase-12 dampens inflammation and neutrophil influx in arthritis.

  2014cites this paper
• Time-resolved Analysis of the Matrix Metalloproteinase 10 Substrate Degradome*

  2013cites this paper
• Matrix metalloproteinase processing of signaling molecules to regulate inflammation.

  2013cites this paper
• Identifying Natural Substrates for Dipeptidyl Peptidases 8 and 9 Using Terminal Amine Isotopic Labeling of Substrates (TAILS) Reveals in Vivo Roles in Cellular Homeostasis and Energy Metabolism

  2013cites this paper
• Homeostasis and Energy Roles in Vivo Substrates ( TAILS ) Reveals Terminal Amine Isotopic Labeling of Dipeptidyl Peptidases 8 and 9 Using Identifying Natural Substrates for Enzymology :

  2013cites this paper
• Proteolytic Post-translational Modification of Proteins: Proteomic Tools and Methodology*

  2013cites this paper
• Systems-Level Analysis of Proteolytic Events in Increased Vascular Permeability and Complement Activation in Skin Inflammation

  2013cites this paper
• Differential isotope dansylation labeling combined with liquid chromatography mass spectrometry for quantification of intact and N-terminal truncated proteins.

  2013cites this paper