Volume 1 Issue 2
Authors: Paul Aiyetan; Bai Zhang; Lily Chen; Zhen Zhang; Hui Zhang
Abstract: Proteome Discoverer is one of many tools used for protein database search and peptide to spectrum assignment in mass spectrometry-based proteomics. However, the inadequacy of conversion tools makes it challenging to compare and integrate its results to those of other analytical tools. Herewith, M2Lite, an open-source, light-weight, easily pluggable and fast conversion tool is presented. M2Lite converts proteome discoverer derived .MSF files to the proteomics community defined standard – the mzIdentML file format. M2Lite’s source code is available as open-source at https://bitbucket.org/paiyetan/m2lite/src and its compiled binaries and documentation can be freely downloaded at https://bitbucket.org/paiyetan/m2lite/downloads.
Keywords: Bioinformatics; Peptide Identification; Proteome Discoverer; MSF; Proteomics; mzIdentML; pepXML; IDPicker
Authors: Jorge Félix Beltrán Lissabet
Abstract: Human Papillomavirus (HPV) classified as high-risk types are implicated in cervical cancer where HPV 16 and HPV 18 are the most frequents among twelve HPV types (16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, and 59) reported by the World Health Organization (WHO). Developments of therapies against HPV-caused malignancies are necessary and depend of the knowledge about how oncogenic HPV drive tumor development and maintenance. The E6 oncoprotein of HPV (HPV E6) interacts with several cellular proteins, activating a number of oncogenic pathways. The determination of HPV E6 three-dimensional structures (HPV E6 3D) opens new opportunities to understand the immunologic mechanisms by which HPV causes infections and drug designing. In this work conformational epitopes of HPV E6 were predicted from HPV E6 3D. Powerful bioinformatics tools like Phyre2, PROCHECK, RAMPAGE, PROSA, ERRAT, SWISS-MODEL Workspace server, ElliPro, and VaxiJen were used in order to predict conformational epitopes with a high quality and reliability. All conformational epitopes obtained principally those with oncogenic antigenicity can be used to a better understanding of the HPV immunology and drug designing.
Keywords: 3D Structure Prediction; E6 Oncoprotein; HPV; Conformational Epitope Prediction