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A new method to analyze matrix‐assisted laser desorption/ionization time‐of‐flight peptide profiling mass spectra
Author(s) -
Dekker Lennard J.,
Dalebout Johannes C.,
Siccama Ivar,
Jenster Guido,
Sillevis Smitt Peter A.,
Luider Theo M.
Publication year - 2005
Publication title -
rapid communications in mass spectrometry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.528
H-Index - 136
eISSN - 1097-0231
pISSN - 0951-4198
DOI - 10.1002/rcm.1864
Subject(s) - reproducibility , chemistry , mass spectrometry , analytical chemistry (journal) , mass spectrum , ionization , chromatography , time of flight mass spectrometry , normalization (sociology) , spectral line , ion , physics , organic chemistry , astronomy , sociology , anthropology
In protein and peptide mass spectrometry in which profiling of peaks is involved, their masses and intensities are important characteristics. Because of the relative low reproducibility of peak intensities associated with complex samples in matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry (MALDI‐TOFMS), it is difficult to accurately assess the number of peaks and their intensities. In this study we evaluate these two characteristics for tryptic digests of cerebro‐spinal fluid. We observed that the reproducibility of peak intensities was relatively poor (CV = 42%) and that additional normalization or spiking did not lead to a large improvement (CV = 30%). Moreover, at least seven mass spectra per sample were required to obtain a reliable peak list. An improvement of the sensitivity (i.e., eventually more peaks are detected) is observed if more replicates per sample are measured. We conclude that the reproducibility and sensitivity of peptide profiling can be significantly improved by a combination of measuring at least seven spectra per sample with a dichotomous scoring of the intensities. This approach will aid the analysis of large numbers of mass spectra of patient samples in a reproducible way for the detection and validation of candidate biomarkers. Copyright © 2005 John Wiley & Sons, Ltd.