Applying Log-Normal Peak Fitting to Parallel Reaction Monitoring Data Analysis

Abstract

Chromatographic separation is often an important part of mass-spectrometry-based proteomic analysis. It reduces the complexity of the initial samples before they are introduced to mass-spectrometric detection and chromatographic characteristics (such as retention time) add analytical features to the analyte. The acquisition and analysis of chromatographic data are thus of great importance, and specialized software is used for the extraction of quantitative information in an efficient and optimized manner. However, occasionally, automatic peak picking and correct peak boundary setting is challenged by, for instance, aberration of peak shape, peak truncation, and peak tailing, and a manual review of a large number of peaks is frequently required. To support this part of the analysis, we present here a software tool, Peakfit, that fits acquired chromatographic data to the log-normal peak equation and reports the calculated peak parameters. The program is written in R and can easily be integrated into Skyline, a popular software packages that is frequently used for proteomic parallel reaction monitoring applications. The program is capable of processing large data sets (>10 000 peaks) and detecting sporadic outliers in peak boundary selection performed, for instance, in Skyline. In an example data set, available via ProteomeXchange with identifier PXD026875, we demonstrated the capability of the program to characterize chromatographic peaks and showed an example of its ability to objectively and reproducibly detect and solve problematic peak-picking situations.

Dynamic monitoring of myeloma minimal residual disease with targeted mass spectrometry

“…Serum samples were digested with trypsin and analyzed with targeted parallel reaction monitoring mass spectrometer. Data were processed with Skyline analysis software, whereby the software tool Peakfit was used to automatically select the correct peptide peak boundaries before data was manually reviewed [ 11 ]. M-protein serum levels were quantified in sera of all 41 patients based on patient-specific clonotypic M-protein peptides (Supplementary Table 2 ).…”