Visualization and analysis of molecular scanner peptide mass spectra

Journal of the American Society for Mass Spectrometry
Markus MüllerDenis F Hochstrasser

Abstract

The molecular scanner combines protein separation using gel electrophoresis with peptide mass fingerprinting (PMF) techniques to identify proteins in a highly automated manner. Proteins separated in a 2-dimensional polyacrylamide gel (2-D PAGE) are digested in parallel and transferred onto a membrane keeping their relative positions. The membrane is then sprayed with a matrix and inserted into a matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometer, which measures a peptide mass fingerprint at each site on the scanned grid. First, visualization of PMF data allows surveying all fingerprints at once and provides very useful information on the presence of chemical noise. Chemical noise is shown to be a potential source for erroneous identifications and is therefore purged from the mass fingerprints. Then, the correlation between neighboring spectra is used to recalibrate the peptide masses. Finally, a method that clusters peptide masses according to the similarity of the spatial distributions of their signal intensities is presented. This method allows discarding many of the false positives that usually go along with PMF identifications and allows identifying many weakly expressed proteins presen...Continue Reading

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Citations

Sep 29, 2011·Journal of the American Society for Mass Spectrometry·Erika R Amstalden van HoveRon M A Heeren
Oct 22, 2003·Clinica Chimica Acta; International Journal of Clinical Chemistry·Laure F MarvinLaurent B Fay
Apr 23, 2004·Current Opinion in Biotechnology·Pierre-Alain BinzRon D Appel
Apr 29, 2010·Chemical Reviews·Kamila Chughtai, Ron M A Heeren
Jan 8, 2004·Clinical Chemistry and Laboratory Medicine : CCLM·Pierre-Alain BinzRon D Appel
Jul 19, 2002·Journal of Mass Spectrometry : JMS
Jan 19, 2007·Journal of Mass Spectrometry : JMS·M Reid GrosecloseRichard M Caprioli
Feb 8, 2006·Mass Spectrometry Reviews·Melanie HilarioMarkus Müller
Apr 11, 2006·Journal of Proteome Research·Rikard AlmJari Häkkinen

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