In vitro Transcription/Translation System: A Versatile Tool in the Search for Missing Proteins

Research output: Contribution to journalArticle

Abstract

Approximately 18% of all human genes purported to encode proteins have not been directly evidenced at the protein level, according to the validation criteria established by neXtProt, and are considered as “missing” proteins. One of the goals of the Chromosome-Centric Human Proteome Project (C-HPP) is to identify as many of these “missing” proteins as possible in human samples using mass spectrometry-based methods. To further this goal, a consortium of C–HPP teams (chromosomes 5, 10, 16 and 19) has joined forces to devise new strategies to identify “missing” proteins by use of a cell-free in vitro transcription/translation system (IVTT). The proposed strategy employs LC-MS/MS data-dependent acquisition (DDA) and targeted selective reaction monitoring (SRM) methods to scrutinize low complexity samples derived from IVTT translation. The optimized assays are then applied to identify “missing” proteins in human cells and tissues. We describe the approach and show proof-of-concept results for development of LC-SRM assays for identification of eighteen “missing” proteins. We believe that the IVTT system, when coupled with downstream mass spectrometric identification, can be applied to identify proteins that have eluded more traditional methods of detection.

Details

Authors
  • Péter Horvatovich
  • Ákos Végvári
  • Justin Saul
  • Jin Park
  • Ji Qiu
  • Michael Syring
  • Patrick Pirrotte
  • Konstantinos Petritis
  • Tony Tegeler
  • Meraj Aziz
  • Manuel Fuentes
  • Paula Diez
  • Maria Gonzalez-Gonzalez
  • Nieves Ibarrola
  • Conrad Droste
  • Javier De Las Rivas
  • Concha Gil
  • Felipe Clemente
  • Maria Luisa Hernaez
  • Fernando Corrales
  • Carol Nilsson
  • Frode Berven
  • Rainer Bischoff
  • Thomas Fehniger
  • Joshua LaBaer
Organisations
Research areas and keywords

Subject classification (UKÄ) – MANDATORY

  • Biological Sciences

Keywords

  • bioinformatics, proteomics, in vitro transcription translation system, LC-MS, chromosome centric human proteome project, missing proteins
Original languageEnglish
Pages (from-to)3441-3451
JournalJournal of Proteome Research
Volume14
Issue number9
Publication statusPublished - 2015
Publication categoryResearch
Peer-reviewedYes