Automated peptide mapping and protein-topographical annotation of proteomics data

BackgroundIn quantitative proteomics, peptide mapping is a valuable approach to combine positional quantitative information with topographical and domain information of proteins. Quantitative proteomic analysis of cell surface shedding is an exemplary application area of this approach.ResultsWe developed ImproViser (http://www.improviser.uni-freiburg.de) for fully automated peptide mapping of quantitative proteomics data in the protXML data. The tool generates sortable and graphically annotated output, which can be easily shared with further users. As an exemplary application, we show its usage in the proteomic analysis of regulated intramembrane proteolysis.ConclusionImproViser is the first tool to enable automated peptide mapping of the widely-used protXML format.

[1]  María Martín,et al.  Activities at the Universal Protein Resource (UniProt) , 2013, Nucleic Acids Res..

[2]  Christian H. Ahrens,et al.  Protter: interactive protein feature visualization and integration with experimental proteomic data , 2014, Bioinform..

[3]  Chris F. Taylor,et al.  A common open representation of mass spectrometry data and its application to proteomics research , 2004, Nature Biotechnology.

[4]  T. Reinheckel,et al.  Double deficiency of cathepsins B and L results in massive secretome alterations and suggests a degradative cathepsin-MMP axis , 2013, Cellular and Molecular Life Sciences.

[5]  R. Aebersold,et al.  A statistical model for identifying proteins by tandem mass spectrometry. , 2003, Analytical chemistry.

[6]  The UniProt Consortium,et al.  Update on activities at the Universal Protein Resource (UniProt) in 2013 , 2012, Nucleic Acids Res..

[7]  E. Hauben,et al.  SPPL2a and SPPL2b promote intramembrane proteolysis of TNFα in activated dendritic cells to trigger IL-12 production , 2006, Nature Cell Biology.

[8]  Daniel R. Beisner,et al.  The intramembrane protease Sppl2a is required for B cell and DC development and survival via cleavage of the invariant chain , 2013, The Journal of experimental medicine.

[9]  Dmitrij Frishman,et al.  QARIP: a web server for quantitative proteomic analysis of regulated intramembrane proteolysis , 2013, Nucleic Acids Res..

[10]  R. Aebersold,et al.  Automated statistical analysis of protein abundance ratios from data generated by stable-isotope dilution and tandem mass spectrometry. , 2003, Analytical chemistry.

[11]  T. Andrews,et al.  B cell survival, surface BCR and BAFFR expression, CD74 metabolism, and CD8− dendritic cells require the intramembrane endopeptidase SPPL2A , 2013, The Journal of experimental medicine.

[12]  Charles Darwin,et al.  Experiments , 1800, The Medical and physical journal.

[13]  E. Birney,et al.  The International Protein Index: An integrated database for proteomics experiments , 2004, Proteomics.

[14]  BMC Bioinformatics , 2005 .

[15]  Christopher M Overall,et al.  Proteomics Discovery of Metalloproteinase Substrates in the Cellular Context by iTRAQ™ Labeling Reveals a Diverse MMP-2 Substrate Degradome*S , 2007, Molecular & Cellular Proteomics.

[16]  B. Fakler,et al.  Extending the Dynamic Range of Label-free Mass Spectrometric Quantification of Affinity Purifications* , 2011, Molecular & Cellular Proteomics.

[17]  Benjamin F. Cravatt,et al.  Global Mapping of the Topography and Magnitude of Proteolytic Events in Apoptosis , 2008, Cell.

[18]  W. Wels,et al.  The Fas ligand intracellular domain is released by ADAM10 and SPPL2a cleavage in T-cells , 2007, Cell Death and Differentiation.

[19]  Patrick G. A. Pedrioli.  Trans-Proteomic Pipeline: A Pipeline for Proteomic Analysis , 2010, Proteome Bioinformatics.

[20]  M. Mann,et al.  MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification , 2008, Nature Biotechnology.

[21]  D. Teplow,et al.  A gamma-secretase-like intramembrane cleavage of TNFalpha by the GxGD aspartyl protease SPPL2b. , 2006, Nature cell biology.

[22]  B. Schröder,et al.  Mechanism, specificity, and physiology of signal peptide peptidase (SPP) and SPP-like proteases. , 2013, Biochimica et biophysica acta.

[23]  Martin L. Biniossek,et al.  Secretome and degradome profiling shows that Kallikrein‐related peptidases 4, 5, 6, and 7 induce TGFβ‐1 signaling in ovarian cancer cells , 2013, Molecular oncology.

[24]  R. Lüllmann-Rauch,et al.  The Intramembrane Proteases Signal Peptide Peptidase-Like 2a and 2b Have Distinct Functions In Vivo , 2014, Molecular and Cellular Biology.

[25]  D. Teplow,et al.  A γ-secretase-like intramembrane cleavage of TNFα by the GxGD aspartyl protease SPPL2b , 2006, Nature Cell Biology.

[26]  T. Reinheckel,et al.  Disrupted in renal carcinoma 2 (DIRC2), a novel transporter of the lysosomal membrane, is proteolytically processed by cathepsin L. , 2011, The Biochemical journal.

[27]  R. Lüllmann-Rauch,et al.  The intramembrane protease SPPL2a promotes B cell development and controls endosomal traffic by cleavage of the invariant chain , 2013, The Journal of experimental medicine.

[28]  R. Aebersold,et al.  Quantitative profiling of differentiation-induced microsomal proteins using isotope-coded affinity tags and mass spectrometry , 2001, Nature Biotechnology.

[29]  Song Li,et al.  WaveletQuant, an improved quantification software based on wavelet signal threshold de-noising for labeled quantitative proteomic analysis , 2010, BMC Bioinformatics.