Publications

Biognosys has expert know-how in the field of Next-Generation Proteomics. Our scientists have participated in several peer-reviewed publications and presentations at international conferences.

 

Presentations at international conferences

Presentations from international conferences are available on Science Hub, a library that contains scientific and technical information related to Biognosys technology, products and services.

 

Peer-reviewed publications

  1. Bruderer R, Sondermann J, Tsou CC, Barrantes-Freer A, Stadelmann C, Nesvizhskii AI, Schmidt M, Reiter L, Gomez-Varela D. New targeted approaches for the quantification of data-independent acquisition mass spectrometry. Proteomics. 2017 Mar 20. 
  2. Rinner O. Next-generation Proteomics from an Industrial Perspective. CHIMIA 2016; 70(2): 860-863.
  3. Kusebauch U, Campbell DS, Deutsch EW, Chu CS, Spicer DA, Brusniak MY, Slagel J, Sun Z, Stevens J, Grimes B, Shteynberg D, Hoopmann MR, Blattmann P, Ratushny AV, Rinner O, et al. Human SRMAtlas: A Resource of Targeted Assays to Quantify the Complete Human Proteome. Cell. 2016; 166(3):766-78. 
  4. Navarro P, Kuharev J, Gillet LC, Bernhardt OM, MacLean B, Röst HL, Tate SA, Tsou CC, Reiter L, et al. A multicenter study benchmarks software tools for label-free proteome quantification. Nat Biotechnol. 2016; 34(11):1130-1136.
  5. Vowinckel J, Zelezniak A, Kibler A, Bruderer R, Muelleder M, Reiter L, Ralser M. Precise label-free quantitative proteomes in high-throughput by microLC and data-independent SWATH acquisition. bioRxiv Sep 5.
  6. Bruderer R, Bernhardt OM, Gandhi T, Reiter L. High-precision iRT prediction in the targeted analysis of data-independent acquisition and its impact on identification and quantitation. Proteomics. 2016; 16(15-16): 2246-56.
  7. Muntel J, Xuan Y, Berger ST, Reiter L, Bachur R, Kentsis A, Steen H. Advancing Urinary Protein Biomarker Discovery by Data-Independent Acquisition on a Quadrupole-Orbitrap Mass Spectrometer. J Proteome Res. 2015; 14(11):4752-4762. 
  8. Krautkramer KA, Reiter L, Denu JM, Dowell JA. Quantification of SAHA-Dependent Changes in Histone Modifications Using Data-Independent Acquisition Mass Spectrometry. J Proteome Res. 2015; 14(8):3252-62.
  9. Sjöström M, Ossola R, Breslin T, Rinner O, Malmström L, Schmidt A, Aebersold R, Malmström J, Niméus E. A Combined Shotgun and Targeted Mass Spectrometry Strategy for Breast Cancer Biomarker Discovery. J Proteome Res. 2015; 14(7):2807-18.
  10. Bruderer R, Bernhardt OM, Gandhi T, Miladinovic SM, Cheng LY, Messner S, et al. Extending the limits of quantitative proteome profiling with data-independent acquisition and application to acetaminophen treated 3D liver microtissues. Mol Cell Proteomics. 2015 Feb 27. pii: mcp.M114.044305.
  11. Selevsek N, Chang CY, Gillet LC, Navarro P, Bernhardt OM, Reiter L, Cheng LY, Vitek O, Aebersold R. Reproducible and consistent quantification of the Saccharomyces cerevisiae proteome by SWATH-mass spectrometry. Mol Cell Proteomics. 2015; 14(3):739-749.
  12. Lebert D, Louwagie M, Goetze S, Picard G, Ossola R, Duquesne C, et al. DIGESTIF: a universal quality standard for the control of bottom-up proteomics experiments. J Proteome Res. 2015; 14(2):787-803.
  13. Carr SA, Abbatiello SE, Ackermann BL et al. Targeted peptide measurements in biology and medicine: best practices for mass spectrometry-based assay development using a fit-for-purpose approach. Mol Cell Proteomics. 2014; 13(3):907-17.
  14. Hüttenheim R, Surinova S, Ossola R, Sun Z, Campbell D, Cerciello F, Schiess R et al.: N-Glycoprotein SRMAtlas: a resource of mass-spectrometric assays for N-glycosites enabling consistent and multiplexed protein quantification for clinical applications, Mol Cell Proteomics, 2013, 12(4):1005-16.
  15. Ori A, Banterle N, Iskar M, Andrés-Pons A, Escher C, Khanh Bui H, Sparks L, Solis-Mezarino V, Rinner O, Bork P, Lemke EA, Beck M. Cell type-specific nuclear pores: a case in point for context-dependent stoichiometry of molecular machines. Mol Syst Biol. 2013; 9:648.
  16. Picotti P, Clément-Ziza M, Lam H, Campbell DS, Schmidt A, Deutsch EW, Röst H, et al: A complete mass-spectrometric map of the yeast proteome applied to quantitative trait analysis,  2013, 494(7436):266-70. 
  17. Karlsson C, Malmström L, Aebersold R, Malmström J: Proteome-wide selected reaction monitoring assays for the human pathogen Streptococcus pyogenes, Nature Communications 2012, 3, article number 1301.
  18. Hüttenhain R, Soste M, Selevsek N, Röst H, Sethi A, Carapito C, Farrah T, Deutsch EW, Kusebauch U, Moritz RL, Nieméus-Malmström E, Rinner O, Aebersold R: Reproducible quantification of cancer-associated proteins in body fluids using targeted proteomics, Science Translational Medicine 2012, 4(142): 142ra94.
  19. Escher C, Reiter L, MacLean B, Ossola R, Herzog F, Chilton J, MacCoss M.J, Rinner O: Using iRT, a normalized retention time for more targeted measurement of peptides, Proteomics 2012, 12(8): 1111-1121.
  20. Gillet LC, Navarro P, Tate S, Röst H, Selevsek N, Reiter L, Bonner R, Aebersold R. Targeted data extraction of the MS/MS spectra generated by data-independent acquisition: a new concept for consistent and accurate proteome analysis. Mol Cell Proteomics. 2012; 11(6): O111.016717.
  21. Reiter L, Rinner O, Picotti P, Huttenhain R, Beck M, Brusniak MY, Hengartner MO, Aebersold R: mProphet: automated data processing and statistical validation for large-scale SRM experiments, Nature methods 2011, 8(5): 430-435.
  22. Ossola R, Schiess R, Picotti P, Rinner O, Reiter L, Aebersold R: Biomarker validation in blood specimens by selected reaction monitoring mass spectrometry of N-glycosites, Methods Mol Biol 2011, 728: 179-194.
  23. Costenoble R, Picotti P, Reiter L, Stallmach R, Heinemann M, Sauer U, Aebersold R: Comprehensive quantitative analysis of central carbon and amino-acid metabolism in Saccharomyces cerevisiae under multiple conditions by targeted proteomics, Mol Syst Biol 2011, 7: 464.
  24. Picotti P, Rinner O, Stallmach R, Dautel F, Farrah T, Domon B, Wenschuh H, Aebersold R: High-throughput generation of selected reaction-monitoring assays for proteins and proteomes, Nature methods 2009, 7(1): 43-46.
  25. Jovanovic M, Reiter L, Picotti P, Lange V, Bogan E, Hurschler BA, Blenkiron C, Lehrbach NJ, Ding XC, Weiss M et al: A quantitative targeted proteomics approach to validate predicted microRNA targets in C. elegans, Nature methods 2010, 7(10): 837-842.
  26. Malmstrom J, Beck M, Schmidt A, Lange V, Deutsch EW, Aebersold R: Proteome-wide cellular protein concentrations of the human pathogen Leptospira interrogans,Nature 2009, 460(7256): 762-765.
  27. Cima I, Schiess R, Wild P, Kaelin M, Schuffler P, Lange V, Picotti P, Ossola R, Templeton A, Schubert O et al: Cancer genetics-guided discovery of serum biomarker signatures for diagnosis and prognosis of prostate cancer, Proc Natl Acad Sci U S A 2011, 108(8): 3342-3347.
  28. Stahl-Zeng J, Lange V, Ossola R, Eckhardt K, Krek W, Aebersold R, Domon B: High sensitivity detection of plasma proteins by multiple reaction monitoring of N-glycosites, Mol Cell Proteomics 2007, 6(10): 1809-1817.
  29. Schrimpf SP, Weiss M, Reiter L, Ahrens CH, Jovanovic M, Malmstrom J, Brunner E, Mohanty S, Lercher MJ, Hunziker PE et al: Comparative functional analysis of the Caenorhabditis elegans and Drosophila melanogaster proteomes, PLoS biology 2009, 7(3): e48.
  30. Reiter L, Claassen M, Schrimpf SP, Jovanovic M, Schmidt A, Buhmann JM, Hengartner MO, Aebersold R: Protein identification false discovery rates for very large proteomics data sets generated by tandem mass spectrometry, Mol Cell Proteomics 2009, 8(11): 2405-2417.
  31. Rinner O, Seebacher J, Walzthoeni T, Mueller LN, Beck M, Schmidt A, Mueller M, Aebersold R: Identification of cross-linked peptides from large sequence databases, Nature methods 2008, 5(4): 315-318.
  32. Soltermann A, Ossola R, Kilgus-Hawelski S, von Eckardstein A, Suter T, Aebersold R, Moch H: N-glycoprotein profiling of lung adenocarcinoma pleural effusions by shotgun proteomics, Cancer 2008, 114(2): 124-133.
  33. Klimek J, Eddes JS, Hohmann L, Jackson J, Peterson A, Letarte S, Gafken PR, Katz JE, Mallick P, Lee H et al: The standard protein mix database: a diverse data set to assist in the production of improved Peptide and protein identification software tools, J Proteome Res 2008, 7(1): 96-103.
  34. Deutsch EW, Eng JK, Zhang H, King NL, Nesvizhskii AI, Lin B, Lee H, Yi EC, Ossola R, Aebersold R: Human Plasma PeptideAtlas, Proteomics 2005, 5(13): 3497-3500.
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