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Automated protein identification by the combination of MALDI MS and MS/MS spectra from different instruments

  • Fredrik Levander
  • Peter James
Publishing year: 2005
Language: English
Pages: 71-74
Publication/Series: Journal of Proteome Research
Volume: 4
Issue: 1
Document type: Journal article
Publisher: The American Chemical Society

Abstract english

The identification of proteins separated on two-dimensional gels is most commonly performed by trypsin digestion and subsequent matrix-assisted laser desorption ionization (MALDI) with time-of-flight (TOF). Recently, atmospheric pressure (AP) MALDI coupled to an ion trap (IT) has emerged as a convenient method to obtain tandem mass spectra (MS/MS) from samples on MALDI target plates. In the present work, we investigated the feasibility of using the two methodologies in line as a standard method for protein identification. In this setup, the high mass accuracy MALDI-TOF spectra are used to calibrate the peptide precursor masses in the lower mass accuracy AP-MALDI-IT MS/MS spectra. Several software tools were developed to automate the analysis process. Two sets of MALDI samples, consisting of 142 and 421 gel spots, respectively, were analyzed in a highly automated manner. In the first set, the protein identification rate increased from 61% for MALDI-TOF only to 85% for MALDI-TOF combined with AP-MALDI-IT. In the second data set the increase in protein identification rate was from 44% to 58%. AP-MALDI-IT MS/MS spectra were in general less effective than the MALDI-TOF spectra for protein identification, but the combination of the two methods clearly enhanced the confidence in protein identification.


  • Immunology in the medical area
  • protein identification
  • ion trap
  • time-of-flight


  • ISSN: 1535-3893
Peter James
E-mail: peter [dot] james [at] immun [dot] lth [dot] se


Department of Immunotechnology

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