Fast pure ion chromatograms extraction method for LC-MS

Liquid chromatography coupled with mass spectrometry (LC-MS) has shown great potential in analysis complex samples. However, informative feature extraction is still challenge since the electrospray ionization in LC-MS tends to produce ninety percent or more ions not originated from compounds of interest. The concept of pure ion chromatogram (PIC) is effective to extract informative ions, but tradition PIC methods are time-consuming because of their theories and programming languages. In this study, we present a novel method, called Fast Pure Ions Chromatograms (FPIC), for extracting PICs from raw LC-MS dataset effectively and quickly. This method can search ion of PIC from its maximum bi-directionally and adaptively, which can improve the stability and reduce the computation time drastically. A further speedup has been achieved by exploiting modern software engineering techniques. FPIC was validated by analyzing four LC-MS datasets: MM14 and MM48, simulated MM48 and quantification (MTBLS234) datasets. Results show that FPIC outperformed traditional methods in the recall, precision and F-score, and it has good reliability of quantification. Furthermore, the method is very fast with few adjustable parameters, which leads to an approximately 125-fold speedup over PITracer and 18-fold speedup over XCMS. An open source implementation of the FPIC method is available at https://github.com/zmzhang/pymass.