
Peter James
Professor

Automated protein identification by the combination of MALDI MS and MS/MS spectra from different instruments
Author
Summary, in 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.
Department/s
- Department of Immunotechnology
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 (ACS)
Topic
- Immunology in the medical area
Keywords
- protein identification
- ion trap
- time-of-flight
- MALDI
- AP-MALDI
Status
Published
ISBN/ISSN/Other
- ISSN: 1535-3893