Literature DB >> 26867746

Selecting Optimal Peptides for Targeted Proteomic Experiments in Human Plasma Using In Vitro Synthesized Proteins as Analytical Standards.

James G Bollinger1, Andrew B Stergachis1, Richard S Johnson1, Jarrett D Egertson1, Michael J MacCoss2.   

Abstract

In targeted proteomics, the development of robust methodologies is dependent upon the selection of a set of optimal peptides for each protein-of-interest. Unfortunately, predicting which peptides and respective product ion transitions provide the greatest signal-to-noise ratio in a particular assay matrix is complicated. Using in vitro synthesized proteins as analytical standards, we report here an empirically driven method for the selection of said peptides in a human plasma assay matrix.

Entities:  

Keywords:  Human plasma proteome; In vitro translation; Proteotypic peptides; Selected reaction monitoring; Targeted proteomics

Mesh：

Substances：

Year:  2016        PMID： 26867746      PMCID： PMC5614897          DOI： 10.1007/978-1-4939-3524-6_12

Source DB:  PubMed          Journal:  Methods Mol Biol        ISSN： 1064-3745


  16 in total

1.  Mass spectrometric quantitation of peptides and proteins using Stable Isotope Standards and Capture by Anti-Peptide Antibodies (SISCAPA).

Authors:  N Leigh Anderson; Norman G Anderson; Lee R Haines; Darryl B Hardie; Robert W Olafson; Terry W Pearson
Journal:  J Proteome Res       Date:  2004 Mar-Apr       Impact factor: 4.466

2.  Computational prediction of proteotypic peptides for quantitative proteomics.

Authors:  Parag Mallick; Markus Schirle; Sharon S Chen; Mark R Flory; Hookeun Lee; Daniel Martin; Jeffrey Ranish; Brian Raught; Robert Schmitt; Thilo Werner; Bernhard Kuster; Ruedi Aebersold
Journal:  Nat Biotechnol       Date:  2006-12-31       Impact factor: 54.908

3.  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

Review 4.  Future prospects for the analysis of complex biological systems using micro-column liquid chromatography-electrospray tandem mass spectrometry.

Authors:  J R Yates; A L McCormack; A J Link; D Schieltz; J Eng; L Hays
Journal:  Analyst       Date:  1996-07       Impact factor: 4.616

5.  Multiplexed absolute quantification in proteomics using artificial QCAT proteins of concatenated signature peptides.

Authors:  Robert J Beynon; Mary K Doherty; Julie M Pratt; Simon J Gaskell
Journal:  Nat Methods       Date:  2005-08       Impact factor: 28.547

6.  Absolute quantification of the model biomarker prostate-specific antigen in serum by LC-Ms/MS using protein cleavage and isotope dilution mass spectrometry.

Authors:  David R Barnidge; Marcia K Goodmanson; George G Klee; David C Muddiman
Journal:  J Proteome Res       Date:  2004 May-Jun       Impact factor: 4.466

7.  A database of mass spectrometric assays for the yeast proteome.

Authors:  Paola Picotti; Henry Lam; David Campbell; Eric W Deutsch; Hamid Mirzaei; Jeff Ranish; Bruno Domon; Ruedi Aebersold
Journal:  Nat Methods       Date:  2008-11       Impact factor: 28.547

8.  Prediction of high-responding peptides for targeted protein assays by mass spectrometry.

Authors:  Vincent A Fusaro; D R Mani; Jill P Mesirov; Steven A Carr
Journal:  Nat Biotechnol       Date:  2009-01-25       Impact factor: 54.908

9.  Using iRT, a normalized retention time for more targeted measurement of peptides.

Authors:  Claudia Escher; Lukas Reiter; Brendan MacLean; Reto Ossola; Franz Herzog; John Chilton; Michael J MacCoss; Oliver Rinner
Journal:  Proteomics       Date:  2012-04       Impact factor: 3.984

10.  Rapid empirical discovery of optimal peptides for targeted proteomics.

Authors:  Andrew B Stergachis; Brendan MacLean; Kristen Lee; John A Stamatoyannopoulos; Michael J MacCoss
Journal:  Nat Methods       Date:  2011-11-06       Impact factor: 28.547
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  5 in total

1.  Analysis of the Proteome of Hair-Cell Stereocilia by Mass Spectrometry.

Authors:  J F Krey; P A Wilmarth; L L David; P G Barr-Gillespie
Journal:  Methods Enzymol       Date:  2016-10-19       Impact factor: 1.600

Review 2.  Deepening our understanding of HDL proteome.

Authors:  Graziella Eliza Ronsein; Tomáš Vaisar
Journal:  Expert Rev Proteomics       Date:  2019-08-27       Impact factor: 3.940

Review 3.  GLOBAL AND TARGETED PROFILING OF GTP-BINDING PROTEINS IN BIOLOGICAL SAMPLES BY MASS SPECTROMETRY.

Authors:  Ming Huang; Yinsheng Wang
Journal:  Mass Spectrom Rev       Date:  2020-06-10       Impact factor: 10.946

4.  Peptide Selection for Accurate Targeted Protein Quantification via a Dimethylation High-Resolution Mass Spectrum Strategy with a Peptide Release Kinetic Model.

Authors:  Qi Chen; Yirong Jiang; Yiping Ren; Meirong Ying; Baiyi Lu
Journal:  ACS Omega       Date:  2020-02-18

5.  Simple Targeted Assays for Metabolic Pathways and Signaling: A Powerful Tool for Targeted Proteomics.

Authors:  Dominik Kopczynski; Andreas Hentschel; Cristina Coman; Nils Helge Schebb; Thorsten Hornemann; Douglas G Mashek; Nicole M Hartung; Olga Shevchuk; Hans-Frieder Schött; Kristina Lorenz; Federico Torta; Bo Burla; René P Zahedi; Albert Sickmann; Michael R Kreutz; Christer S Ejsing; Jan Medenbach; Robert Ahrends
Journal:  Anal Chem       Date:  2020-09-21       Impact factor: 6.986
  5 in total

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