Peter Pichler

Summary

Affiliation: University of Vienna
Country: Austria

Publications

  1. pmc Peptide labeling with isobaric tags yields higher identification rates using iTRAQ 4-plex compared to TMT 6-plex and iTRAQ 8-plex on LTQ Orbitrap
    Peter Pichler
    Christian Doppler Laboratory for Proteome Analysis, University of Vienna, Austria
    Anal Chem 82:6549-58. 2010
  2. pmc Improved precision of iTRAQ and TMT quantification by an axial extraction field in an Orbitrap HCD cell
    Peter Pichler
    Christian Doppler Laboratory for Proteome Analysis, University of Vienna, Vienna, Austria
    Anal Chem 83:1469-74. 2011
  3. doi Proteomic analysis reveals a virtually complete set of proteins for translation and energy generation in elementary bodies of the amoeba symbiont Protochlamydia amoebophila
    Barbara S Sixt
    Department of Microbial Ecology, University of Vienna, Vienna, Austria
    Proteomics 11:1868-92. 2011
  4. doi Altered Mascot search results by changing the m/z range of MS/MS spectra: analysis and potential applications
    Thomas Kocher
    Research Institute of Molecular Pathology IMP, Vienna, Austria
    Anal Bioanal Chem 400:2339-47. 2011
  5. pmc Identification and characterization of a novel porin family highlights a major difference in the outer membrane of chlamydial symbionts and pathogens
    Karin Aistleitner
    Department of Microbial Ecology, University of Vienna, Vienna, Austria
    PLoS ONE 8:e55010. 2013
  6. doi Analysis of protein mixtures from whole-cell extracts by single-run nanoLC-MS/MS using ultralong gradients
    Thomas Kocher
    Research Institute of Molecular Pathology, Vienna, Austria
    Nat Protoc 7:882-90. 2012
  7. pmc SIMPATIQCO: a server-based software suite which facilitates monitoring the time course of LC-MS performance metrics on Orbitrap instruments
    Peter Pichler
    Research Institute of Molecular Pathology, Vienna, Austria
    J Proteome Res 11:5540-7. 2012
  8. doi General statistical modeling of data from protein relative expression isobaric tags
    Florian P Breitwieser
    CeMM, Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
    J Proteome Res 10:2758-66. 2011
  9. doi High precision quantitative proteomics using iTRAQ on an LTQ Orbitrap: a new mass spectrometric method combining the benefits of all
    Thomas Kocher
    Research Institute of Molecular Pathology IMP, Vienna, Austria
    J Proteome Res 8:4743-52. 2009
  10. doi Development and performance evaluation of an ultralow flow nanoliquid chromatography-tandem mass spectrometry set-up
    Thomas Kocher
    Research Institute of Molecular Pathology IMP, Vienna, Austria
    Proteomics 14:1999-2007. 2014

Collaborators

Detail Information

Publications16

  1. pmc Peptide labeling with isobaric tags yields higher identification rates using iTRAQ 4-plex compared to TMT 6-plex and iTRAQ 8-plex on LTQ Orbitrap
    Peter Pichler
    Christian Doppler Laboratory for Proteome Analysis, University of Vienna, Austria
    Anal Chem 82:6549-58. 2010
    ..These fragment ions cannot be explained by current search engines and were observed to have a negative impact on peptide scores...
  2. pmc Improved precision of iTRAQ and TMT quantification by an axial extraction field in an Orbitrap HCD cell
    Peter Pichler
    Christian Doppler Laboratory for Proteome Analysis, University of Vienna, Vienna, Austria
    Anal Chem 83:1469-74. 2011
    ..These findings may help researchers in their design of quantitative proteomics studies using isobaric tags and establish HCD-based quantification on the LTQ Orbitrap as a highly precise approach in quantitative proteomics...
  3. doi Proteomic analysis reveals a virtually complete set of proteins for translation and energy generation in elementary bodies of the amoeba symbiont Protochlamydia amoebophila
    Barbara S Sixt
    Department of Microbial Ecology, University of Vienna, Vienna, Austria
    Proteomics 11:1868-92. 2011
    ..amoebophila exploits its additional genetic repertoire (compared with the Chlamydiaceae), and that its elementary bodies are remarkably well equipped with proteins involved in transcription, translation, and energy generation...
  4. doi Altered Mascot search results by changing the m/z range of MS/MS spectra: analysis and potential applications
    Thomas Kocher
    Research Institute of Molecular Pathology IMP, Vienna, Austria
    Anal Bioanal Chem 400:2339-47. 2011
    ..We further show that the effect can be exploited and additional proteins and peptides can be identified by repeating the search with a combined set of differently processed files, even when applying identical false-positive rates...
  5. pmc Identification and characterization of a novel porin family highlights a major difference in the outer membrane of chlamydial symbionts and pathogens
    Karin Aistleitner
    Department of Microbial Ecology, University of Vienna, Vienna, Austria
    PLoS ONE 8:e55010. 2013
    ..amoebophila. This work contributes to our understanding of the adaptations of symbiotic and pathogenic chlamydiae to their different eukaryotic hosts...
  6. doi Analysis of protein mixtures from whole-cell extracts by single-run nanoLC-MS/MS using ultralong gradients
    Thomas Kocher
    Research Institute of Molecular Pathology, Vienna, Austria
    Nat Protoc 7:882-90. 2012
    ..Demonstrating the practical applicability of the method, we identified 2,761 proteins from a HeLa cell lysate, requiring around 10 h of nanoLC-MS/MS measurement time...
  7. pmc SIMPATIQCO: a server-based software suite which facilitates monitoring the time course of LC-MS performance metrics on Orbitrap instruments
    Peter Pichler
    Research Institute of Molecular Pathology, Vienna, Austria
    J Proteome Res 11:5540-7. 2012
    ..The SIMPATIQCO software package is available free of charge...
  8. doi General statistical modeling of data from protein relative expression isobaric tags
    Florian P Breitwieser
    CeMM, Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
    J Proteome Res 10:2758-66. 2011
    ..The isobar package can also be used as an independent software that requires very little or no R programming skills...
  9. doi High precision quantitative proteomics using iTRAQ on an LTQ Orbitrap: a new mass spectrometric method combining the benefits of all
    Thomas Kocher
    Research Institute of Molecular Pathology IMP, Vienna, Austria
    J Proteome Res 8:4743-52. 2009
    ..The new method was applied to study changes in protein expression in mouse hearts upon transverse aortic constriction, a model for cardiac stress...
  10. doi Development and performance evaluation of an ultralow flow nanoliquid chromatography-tandem mass spectrometry set-up
    Thomas Kocher
    Research Institute of Molecular Pathology IMP, Vienna, Austria
    Proteomics 14:1999-2007. 2014
    ..All MS data have been deposited in the ProteomeXchange with identifier PXD000396 (http://proteomecentral.proteomexchange.org/dataset/PXD000396)...
  11. doi Validation of regulated protein phosphorylation events in yeast by quantitative mass spectrometry analysis of purified proteins
    Wolfgang Reiter
    Department for Biochemistry, Max F Perutz Laboratories, University of Vienna, Vienna, Austria
    Proteomics 12:3030-43. 2012
    ..The study of Pan1 under osmotic stress conditions in different mutant backgrounds allowed us to differentiate between mitogen-activated protein kinase Hog1 driven and Hog1 independent stress responses...
  12. doi Quality control in LC-MS/MS
    Thomas Kocher
    Research Institute of Molecular Pathology, Vienna, Austria
    Proteomics 11:1026-30. 2011
    ..Quality control is rarely discussed in scientific publications. Here, we briefly present measures undertaken in our laboratory to foster a general discussion of the subject...
  13. pmc Lesson from the stoichiometry determination of the cohesin complex: a short protease mediated elution increases the recovery from cross-linked antibody-conjugated beads
    Johann Holzmann
    Research Institute of Molecular Pathology IMP, Vienna, Austria
    J Proteome Res 10:780-9. 2011
    ..In summary, we show that the protease elution protocol increases the recovery from affinity beads and is compatible with quantitative measurements such as the stoichiometry determination of protein complexes...
  14. pmc Quantitative Phosphoproteomics of the Ataxia Telangiectasia-Mutated (ATM) and Ataxia Telangiectasia-Mutated and Rad3-related (ATR) Dependent DNA Damage Response in Arabidopsis thaliana
    Elisabeth Roitinger
    From the Institute of Molecular Pathology IMP, Vienna, Austria Institute of Molecular Biotechnology IMBA, Vienna, Austria
    Mol Cell Proteomics 14:556-71. 2015
    ....
  15. doi Proteomic analysis of the outer membrane of Protochlamydia amoebophila elementary bodies
    Eva Heinz
    Department of Microbial Ecology, Faculty of Life Sciences, University of Vienna, Austria
    Proteomics 10:4363-76. 2010
    ..They reveal both fundamental differences and convergent evolution between pathogenic and symbiotic chlamydiae...
  16. doi Raman microspectroscopy reveals long-term extracellular activity of Chlamydiae
    Susanne Haider
    Department of Microbial Ecology, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
    Mol Microbiol 77:687-700. 2010
    ..These findings change our perception of chlamydial biology and reveal that host-free analyses possess a previously not recognized potential for direct experimental access to these elusive microorganisms...