Literature DB >> 29623005

Challenges and Opportunities for Biological Mass Spectrometry Core Facilities in the Developing World.

Liam Bell1, Bridget Calder2, Reinhard Hiller1, Ashwil Klein3, Nelson C Soares2, Stoyan H Stoychev4, Barend C Vorster5, David L Tabb6.   

Abstract

The developing world is seeing rapid growth in the availability of biological mass spectrometry (MS), particularly through core facilities. As proteomics and metabolomics becomes locally feasible for investigators in these nations, application areas associated with high burden in these nations, such as infectious disease, will see greatly increased research output. This article evaluates the rapid growth of MS in South Africa (currently approaching 20 laboratories) as a model for establishing MS core facilities in other nations of the developing world. Facilities should emphasize new services rather than new instruments. The reduction of the delays associated with reagent and other supply acquisition would benefit both facilities and the users who make use of their services. Instrument maintenance and repair, often mediated by an in-country business for an international vendor, is also likely to operate on a slower schedule than in the wealthiest nations. A key challenge to facilities in the developing world is educating potential facility users in how best to design experiments for proteomics and metabolomics, what reagents are most likely to introduce problematic artifacts, and how to interpret results from the facility. Here, we summarize the experience of 6 different institutions to raise the level of biological MS available to researchers in South Africa.

Entities:  

Keywords:  South Africa; capacity development; publication standards; shared instruments

Mesh:

Year:  2018        PMID: 29623005      PMCID: PMC5865507          DOI: 10.7171/jbt.18-2901-003

Source DB:  PubMed          Journal:  J Biomol Tech        ISSN: 1524-0215


  38 in total

Review 1.  Proteomics: the move to mixtures.

Authors:  J Peng; S P Gygi
Journal:  J Mass Spectrom       Date:  2001-10       Impact factor: 1.982

Review 2.  Metabolomics--the link between genotypes and phenotypes.

Authors:  Oliver Fiehn
Journal:  Plant Mol Biol       Date:  2002-01       Impact factor: 4.076

3.  Geographical focus. Proteomics initiatives in Spain: ProteoRed.

Authors:  Alberto Paradela; Pedro-Ramón Escuredo; Juan-Pablo Albar
Journal:  Proteomics       Date:  2006-09       Impact factor: 3.984

4.  The Paragon Algorithm, a next generation search engine that uses sequence temperature values and feature probabilities to identify peptides from tandem mass spectra.

Authors:  Ignat V Shilov; Sean L Seymour; Alpesh A Patel; Alex Loboda; Wilfred H Tang; Sean P Keating; Christie L Hunter; Lydia M Nuwaysir; Daniel A Schaeffer
Journal:  Mol Cell Proteomics       Date:  2007-05-27       Impact factor: 5.911

5.  mzML: a single, unifying data format for mass spectrometer output.

Authors:  Eric Deutsch
Journal:  Proteomics       Date:  2008-07       Impact factor: 3.984

Review 6.  Proteomics in South Africa: current status, challenges and prospects.

Authors:  Bongani K Ndimba; Ludivine A Thomas
Journal:  Biotechnol J       Date:  2008-11       Impact factor: 4.677

7.  Multi-site assessment of the precision and reproducibility of multiple reaction monitoring-based measurements of proteins in plasma.

Authors:  Terri A Addona; Susan E Abbatiello; Birgit Schilling; Steven J Skates; D R Mani; David M Bunk; Clifford H Spiegelman; Lisa J Zimmerman; Amy-Joan L Ham; Hasmik Keshishian; Steven C Hall; Simon Allen; Ronald K Blackman; Christoph H Borchers; Charles Buck; Helene L Cardasis; Michael P Cusack; Nathan G Dodder; Bradford W Gibson; Jason M Held; Tara Hiltke; Angela Jackson; Eric B Johansen; Christopher R Kinsinger; Jing Li; Mehdi Mesri; Thomas A Neubert; Richard K Niles; Trenton C Pulsipher; David Ransohoff; Henry Rodriguez; Paul A Rudnick; Derek Smith; David L Tabb; Tony J Tegeler; Asokan M Variyath; Lorenzo J Vega-Montoto; Asa Wahlander; Sofia Waldemarson; Mu Wang; Jeffrey R Whiteaker; Lei Zhao; N Leigh Anderson; Susan J Fisher; Daniel C Liebler; Amanda G Paulovich; Fred E Regnier; Paul Tempst; Steven A Carr
Journal:  Nat Biotechnol       Date:  2009-06-28       Impact factor: 54.908

8.  METLIN: a metabolite mass spectral database.

Authors:  Colin A Smith; Grace O'Maille; Elizabeth J Want; Chuan Qin; Sunia A Trauger; Theodore R Brandon; Darlene E Custodio; Ruben Abagyan; Gary Siuzdak
Journal:  Ther Drug Monit       Date:  2005-12       Impact factor: 3.681

9.  Metabolic profiling, metabolomic and metabonomic procedures for NMR spectroscopy of urine, plasma, serum and tissue extracts.

Authors:  Olaf Beckonert; Hector C Keun; Timothy M D Ebbels; Jacob Bundy; Elaine Holmes; John C Lindon; Jeremy K Nicholson
Journal:  Nat Protoc       Date:  2007       Impact factor: 13.491

10.  A HUPO test sample study reveals common problems in mass spectrometry-based proteomics.

Authors:  Alexander W Bell; Eric W Deutsch; Catherine E Au; Robert E Kearney; Ron Beavis; Salvatore Sechi; Tommy Nilsson; John J M Bergeron
Journal:  Nat Methods       Date:  2009-06       Impact factor: 28.547

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  3 in total

Review 1.  Clinical Chemistry for Developing Countries: Mass Spectrometry.

Authors:  Suji Lee; Kavyasree Chintalapudi; Abraham K Badu-Tawiah
Journal:  Annu Rev Anal Chem (Palo Alto Calif)       Date:  2021-07-27       Impact factor: 10.745

2.  Nontargeted mass spectrometry of dried blood spots for interrogation of the human circulating metabolome.

Authors:  Casey Ward; Shriram Nallamshetty; Jeramie D Watrous; Eowyn Acres; Tao Long; Ian T Mathews; Sonia Sharma; Susan Cheng; Farhad Imam; Mohit Jain
Journal:  J Mass Spectrom       Date:  2021-05-27       Impact factor: 2.394

Review 3.  Review of the Use of Liquid Chromatography-Tandem Mass Spectrometry in Clinical Laboratories: Part II-Operations.

Authors:  Brian A Rappold
Journal:  Ann Lab Med       Date:  2022-09-01       Impact factor: 4.941

  3 in total

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