Improved method for peak picking in matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

A method for peak picking for matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) is described. The method is based on the assumption that two sets of ions are formed during the ionization stage, which have Gaussian distributions but different velocity profiles. This gives rise to a certain degree of peak skewness. Our algorithm deconvolutes the peak and utilizes the fast velocity, bulk ion distribution for peak picking. Evaluation of the performance of the new method was conducted using peptide peaks from a bovine serum albumin (BSA) digest, and compared with the commercial peak-picking algorithms Centroid and SNAP. When using the new two-Gaussian algorithm, for strong signals the mass accuracy was equal to or marginally better than the results obtained from the commercial algorithms. However, for weak, distorted peaks, considerable improvement in both mass accuracy and precision was obtained. This improvement should be particularly useful in proteomics, where a lack of signal strength is often encountered when dealing with weakly expressed proteins. Finally, since the new peak-picking method uses information from the entire signal, no adjustments of parameters related to peak height have to be made, which simplifies its practical use.