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

Horvatovich, Péter; Végvári, Ákos LU ; Saul, Justin; Park, Jin; Qiu, Ji; Syring, Michael; Pirrotte, Patrick; Petritis, Konstantinos; Tegeler, Tony and Aziz, Meraj, et al. (2015) In Journal of Proteome Research 14(9). p.3441-3451
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... (More)
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. (Less)
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published
subject
keywords
bioinformatics, proteomics, in vitro transcription translation system, LC-MS, chromosome centric human proteome project, missing proteins
in
Journal of Proteome Research
volume
14
issue
9
pages
3441 - 3451
publisher
The American Chemical Society
external identifiers
  • wos:000361087100004
  • scopus:84941060077
ISSN
1535-3893
DOI
10.1021/acs.jproteome.5b00486
language
English
LU publication?
yes
id
3fbea94d-315f-4f5a-a8a4-3153d44f7f90 (old id 7520337)
date added to LUP
2015-08-04 10:35:33
date last changed
2017-11-19 03:21:43
@article{3fbea94d-315f-4f5a-a8a4-3153d44f7f90,
  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.},
  author       = {Horvatovich, Péter and Végvári, Ákos and Saul, Justin and Park, Jin and Qiu, Ji and Syring, Michael and Pirrotte, Patrick and Petritis, Konstantinos and Tegeler, Tony and Aziz, Meraj and Fuentes, Manuel and Diez, Paula and Gonzalez-Gonzalez, Maria and Ibarrola, Nieves and Droste, Conrad and De Las Rivas, Javier and Gil, Concha and Clemente, Felipe and Hernaez, Maria Luisa and Corrales, Fernando and Nilsson, Carol and Berven, Frode and Bischoff, Rainer and Fehniger, Thomas and LaBaer, Joshua and Marko-Varga, György},
  issn         = {1535-3893},
  keyword      = {bioinformatics,proteomics,in vitro transcription translation system,LC-MS,chromosome centric human proteome project,missing proteins},
  language     = {eng},
  number       = {9},
  pages        = {3441--3451},
  publisher    = {The American Chemical Society},
  series       = {Journal of Proteome Research},
  title        = {In vitro Transcription/Translation System: A Versatile Tool in the Search for Missing Proteins},
  url          = {http://dx.doi.org/10.1021/acs.jproteome.5b00486},
  volume       = {14},
  year         = {2015},
}