The Experts below are selected from a list of 210 Experts worldwide ranked by ideXlab platform

Knut Reinert - One of the best experts on this subject based on the ideXlab platform.

  • Calibration of mass spectrometric peptide mass Fingerprint data without specific external or internal calibrants
    BMC Bioinformatics, 2005
    Co-Authors: Witold E Wolski, Maciej Lalowski, Peter Jungblut, Knut Reinert
    Abstract:

    Background Peptide Mass Fingerprinting (PMF) is a widely used mass spectrometry (MS) method of analysis of proteins and peptides. It relies on the comparison between experimentally determined and theoretical mass spectra. The PMF process requires calibration, usually performed with external or internal calibrants of known molecular masses. Results We have introduced two novel MS calibration methods. The first method utilises the local similarity of peptide maps generated after separation of complex protein samples by two-dimensional gel electrophoresis. It computes a multiple peak-list alignment of the data set using a modified Minimum Spanning Tree (MST) algorithm. The second method exploits the idea that hundreds of MS samples are measured in parallel on one sample support. It improves the calibration coefficients by applying a two-dimensional Thin Plate Splines (TPS) smoothing algorithm. We studied the novel calibration methods utilising data generated by three different MALDI-TOF-MS instruments. We demonstrate that a PMF data set can be calibrated without resorting to external or relying on widely occurring internal calibrants. The methods developed here were implemented in R and are part of the BioConductor package mscalib available from http://www.bioconductor.org . Conclusion The MST calibration algorithm is well suited to calibrate MS spectra of protein samples resulting from two-dimensional gel electrophoretic separation. The TPS based calibration algorithm might be used to correct systematic mass measurement errors observed for large MS sample supports. As compared to other methods, our combined MS spectra calibration strategy increases the peptide/protein identification rate by an additional 5 – 15%.

  • Calibration of mass spectrometric peptide mass Fingerprint data without specific external or internal calibrants
    BMC Bioinformatics, 2005
    Co-Authors: Witold E Wolski, Maciej Lalowski, Peter Jungblut, Knut Reinert
    Abstract:

    Background Peptide Mass Fingerprinting (PMF) is a widely used mass spectrometry (MS) method of analysis of proteins and peptides. It relies on the comparison between experimentally determined and theoretical mass spectra. The PMF process requires calibration, usually performed with external or internal calibrants of known molecular masses.

Witold E Wolski - One of the best experts on this subject based on the ideXlab platform.

  • Calibration of mass spectrometric peptide mass Fingerprint data without specific external or internal calibrants
    BMC Bioinformatics, 2005
    Co-Authors: Witold E Wolski, Maciej Lalowski, Peter Jungblut, Knut Reinert
    Abstract:

    Background Peptide Mass Fingerprinting (PMF) is a widely used mass spectrometry (MS) method of analysis of proteins and peptides. It relies on the comparison between experimentally determined and theoretical mass spectra. The PMF process requires calibration, usually performed with external or internal calibrants of known molecular masses. Results We have introduced two novel MS calibration methods. The first method utilises the local similarity of peptide maps generated after separation of complex protein samples by two-dimensional gel electrophoresis. It computes a multiple peak-list alignment of the data set using a modified Minimum Spanning Tree (MST) algorithm. The second method exploits the idea that hundreds of MS samples are measured in parallel on one sample support. It improves the calibration coefficients by applying a two-dimensional Thin Plate Splines (TPS) smoothing algorithm. We studied the novel calibration methods utilising data generated by three different MALDI-TOF-MS instruments. We demonstrate that a PMF data set can be calibrated without resorting to external or relying on widely occurring internal calibrants. The methods developed here were implemented in R and are part of the BioConductor package mscalib available from http://www.bioconductor.org . Conclusion The MST calibration algorithm is well suited to calibrate MS spectra of protein samples resulting from two-dimensional gel electrophoretic separation. The TPS based calibration algorithm might be used to correct systematic mass measurement errors observed for large MS sample supports. As compared to other methods, our combined MS spectra calibration strategy increases the peptide/protein identification rate by an additional 5 – 15%.

  • Calibration of mass spectrometric peptide mass Fingerprint data without specific external or internal calibrants
    BMC Bioinformatics, 2005
    Co-Authors: Witold E Wolski, Maciej Lalowski, Peter Jungblut, Knut Reinert
    Abstract:

    Background Peptide Mass Fingerprinting (PMF) is a widely used mass spectrometry (MS) method of analysis of proteins and peptides. It relies on the comparison between experimentally determined and theoretical mass spectra. The PMF process requires calibration, usually performed with external or internal calibrants of known molecular masses.

Guenther K. Bonn - One of the best experts on this subject based on the ideXlab platform.

  • Solid‐phase extraction of plant thionins employing aluminum silicate based extraction columns
    Journal of Separation Science, 2014
    Co-Authors: Shah Hussain, Yüksel Güzel, Matthias Rainer, Christian W. Huck, Christoph Pezzei, Guenther K. Bonn
    Abstract:

    Thionins belong to a family of cysteine-rich, low-molecular-weight (∼5 KDa) biologically active proteins in the plant kingdom. They display a broad cellular toxicity against a wide range of organisms and eukaryotic cell lines. Thionins protect plants against different pathogens, including bacteria and fungi. A highly selective solid-phase extraction method for plant thionins is reported deploying aluminum silicate (3:2 mullite) powder as a sorbent in extraction columns. Mullite was shown to considerably improve selectivity compared to a previously described zirconium silicate embedded poly(styrene-co-divinylbenzene) monolithic polymer. Due to the presence of aluminum(III), mullite offers electrostatic interactions for the selective isolation of cysteine-rich proteins. In comparison to zirconium(IV) silicate, aluminum(III) silicate showed reduced interactions towards proteins which resulted into superior washings of unspecific compounds while still retaining cysteine-rich thionins. In the presented study, European mistletoe, wheat and barley samples were subjected to solid-phase extraction analysis for isolation of viscotoxins, purothionins and hordothionins, respectively. Matrix-assisted laser desorption/ionization time of flight mass spectroscopy was used for determining the selectivity of the sorbent toward thionins. The selectively retained thionins were quantified by colorimetric detection using the bicinchoninic acid assay. For peptide mass-Fingerprint analysis tryptic digests of eluates were examined.

  • Solid-phase extraction of plant thionins employing aluminum silicate based extraction columns.
    IEEE Journal of Solid-state Circuits, 2014
    Co-Authors: Shah Hussain, Yüksel Güzel, Matthias Rainer, Christian W. Huck, Christoph Pezzei, Guenther K. Bonn
    Abstract:

    : Thionins belong to a family of cysteine-rich, low-molecular-weight (∼5 KDa) biologically active proteins in the plant kingdom. They display a broad cellular toxicity against a wide range of organisms and eukaryotic cell lines. Thionins protect plants against different pathogens, including bacteria and fungi. A highly selective solid-phase extraction method for plant thionins is reported deploying aluminum silicate (3:2 mullite) powder as a sorbent in extraction columns. Mullite was shown to considerably improve selectivity compared to a previously described zirconium silicate embedded poly(styrene-co-divinylbenzene) monolithic polymer. Due to the presence of aluminum(III), mullite offers electrostatic interactions for the selective isolation of cysteine-rich proteins. In comparison to zirconium(IV) silicate, aluminum(III) silicate showed reduced interactions towards proteins which resulted into superior washings of unspecific compounds while still retaining cysteine-rich thionins. In the presented study, European mistletoe, wheat and barley samples were subjected to solid-phase extraction analysis for isolation of viscotoxins, purothionins and hordothionins, respectively. Matrix-assisted laser desorption/ionization time of flight mass spectroscopy was used for determining the selectivity of the sorbent toward thionins. The selectively retained thionins were quantified by colorimetric detection using the bicinchoninic acid assay. For peptide mass-Fingerprint analysis tryptic digests of eluates were examined.

Maciej Lalowski - One of the best experts on this subject based on the ideXlab platform.

  • Calibration of mass spectrometric peptide mass Fingerprint data without specific external or internal calibrants
    BMC Bioinformatics, 2005
    Co-Authors: Witold E Wolski, Maciej Lalowski, Peter Jungblut, Knut Reinert
    Abstract:

    Background Peptide Mass Fingerprinting (PMF) is a widely used mass spectrometry (MS) method of analysis of proteins and peptides. It relies on the comparison between experimentally determined and theoretical mass spectra. The PMF process requires calibration, usually performed with external or internal calibrants of known molecular masses. Results We have introduced two novel MS calibration methods. The first method utilises the local similarity of peptide maps generated after separation of complex protein samples by two-dimensional gel electrophoresis. It computes a multiple peak-list alignment of the data set using a modified Minimum Spanning Tree (MST) algorithm. The second method exploits the idea that hundreds of MS samples are measured in parallel on one sample support. It improves the calibration coefficients by applying a two-dimensional Thin Plate Splines (TPS) smoothing algorithm. We studied the novel calibration methods utilising data generated by three different MALDI-TOF-MS instruments. We demonstrate that a PMF data set can be calibrated without resorting to external or relying on widely occurring internal calibrants. The methods developed here were implemented in R and are part of the BioConductor package mscalib available from http://www.bioconductor.org . Conclusion The MST calibration algorithm is well suited to calibrate MS spectra of protein samples resulting from two-dimensional gel electrophoretic separation. The TPS based calibration algorithm might be used to correct systematic mass measurement errors observed for large MS sample supports. As compared to other methods, our combined MS spectra calibration strategy increases the peptide/protein identification rate by an additional 5 – 15%.

  • Calibration of mass spectrometric peptide mass Fingerprint data without specific external or internal calibrants
    BMC Bioinformatics, 2005
    Co-Authors: Witold E Wolski, Maciej Lalowski, Peter Jungblut, Knut Reinert
    Abstract:

    Background Peptide Mass Fingerprinting (PMF) is a widely used mass spectrometry (MS) method of analysis of proteins and peptides. It relies on the comparison between experimentally determined and theoretical mass spectra. The PMF process requires calibration, usually performed with external or internal calibrants of known molecular masses.

Peter Jungblut - One of the best experts on this subject based on the ideXlab platform.

  • Calibration of mass spectrometric peptide mass Fingerprint data without specific external or internal calibrants
    BMC Bioinformatics, 2005
    Co-Authors: Witold E Wolski, Maciej Lalowski, Peter Jungblut, Knut Reinert
    Abstract:

    Background Peptide Mass Fingerprinting (PMF) is a widely used mass spectrometry (MS) method of analysis of proteins and peptides. It relies on the comparison between experimentally determined and theoretical mass spectra. The PMF process requires calibration, usually performed with external or internal calibrants of known molecular masses. Results We have introduced two novel MS calibration methods. The first method utilises the local similarity of peptide maps generated after separation of complex protein samples by two-dimensional gel electrophoresis. It computes a multiple peak-list alignment of the data set using a modified Minimum Spanning Tree (MST) algorithm. The second method exploits the idea that hundreds of MS samples are measured in parallel on one sample support. It improves the calibration coefficients by applying a two-dimensional Thin Plate Splines (TPS) smoothing algorithm. We studied the novel calibration methods utilising data generated by three different MALDI-TOF-MS instruments. We demonstrate that a PMF data set can be calibrated without resorting to external or relying on widely occurring internal calibrants. The methods developed here were implemented in R and are part of the BioConductor package mscalib available from http://www.bioconductor.org . Conclusion The MST calibration algorithm is well suited to calibrate MS spectra of protein samples resulting from two-dimensional gel electrophoretic separation. The TPS based calibration algorithm might be used to correct systematic mass measurement errors observed for large MS sample supports. As compared to other methods, our combined MS spectra calibration strategy increases the peptide/protein identification rate by an additional 5 – 15%.

  • Calibration of mass spectrometric peptide mass Fingerprint data without specific external or internal calibrants
    BMC Bioinformatics, 2005
    Co-Authors: Witold E Wolski, Maciej Lalowski, Peter Jungblut, Knut Reinert
    Abstract:

    Background Peptide Mass Fingerprinting (PMF) is a widely used mass spectrometry (MS) method of analysis of proteins and peptides. It relies on the comparison between experimentally determined and theoretical mass spectra. The PMF process requires calibration, usually performed with external or internal calibrants of known molecular masses.