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

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.

• Författare: Fredrik Levander; Peter James
• Avdelning/ar: Institutionen för immunteknologi
• Publiceringsår: 2005
• Språk: Engelska
• Sidor: 71-74
• Publikation/Tidskrift/Serie: Journal of Proteome Research
• Volym: 4
• Issue: 1
• Länkar: http://dx.doi.org/10.1021/pr0498584
• Dokumenttyp: Artikel i tidskrift
• Förlag: The American Chemical Society (ACS)
• Ämne: Immunology in the medical area
• Nyckelord: protein identification; ion trap; time-of-flight; MALDI; AP-MALDI
• Status: Published
• ISBN/ISSN/Övrigt: ISSN: 1535-3893