Themis: Batch Preprocessing for Ultrahigh-Resolution Mass Spectra of Complex Mixtures

Abstract

Fourier transform ion cyclotron resonance mass spectrometry affords the resolving power to determine an unprecedented number of components in complex mixtures, such as petroleum. The software tools required to also analyze these data struggle to keep pace with advancing instrument capabilities and increasing quantities of data, particularly in terms of combining information efficiently across multiple replicates. Improved confidence in data and the use of replicates is particularly important where strategic decisions will be based upon the analysis. We present a new algorithm named Themis, developed using R, to jointly preprocess replicate measurements of a sample with the aim of improving consistency as a preliminary step to assigning peaks to chemical compositions. The main features of the algorithm are quality control criteria to detect failed runs, ensuring comparable magnitudes across replicates, peak alignment, and the use of an adaptive mixture model-based strategy to help distinguish true peaks from noise. The algorithm outputs a list of peaks reliably observed across replicates and facilitates data handling by preprocessing all replicates in a single step. The processed data produced by our algorithm can subsequently be analyzed by use of relevant specialized software. While Themis has been demonstrated with petroleum as an example of a complex mixture, its basic framework will be useful for complex samples arising from a variety of other applications.

KairosMS: A New Solution for the Processing of Hyphenated Ultrahigh Resolution Mass Spectrometry Data

“…The Themis algorithm was adapted to work through an additional dimension to perform the denoising and extract each EIC. As previously described, the m / z consistency was used but this time between scans to isolate the EICs.…”

“…Previous work demonstrated that peak list data and R can be used to develop new processing methods which improve the quality of the data. 41 So, to address these issues, we developed a method in the open source language R that can run from either a personal computer (PC) or a web application named KairosMS. The name derives from Kairos, an ancient Greek word used to describe time along with Chronos.…”

“…As previously described, the m/z consistency was used but this time between scans to isolate the EICs. The difference was that due to intensity variations inherent to the chromatography elution, the intensity parameter had to be excluded from the equation used by Gavard et al 41 The method performed well in those conditions, but a threshold for the minimum number of consecutive peaks had to be implemented to reduce false positive EICs arising from the combination of too few data points. The user can adjust this parameter by considering the experiment hardware, the sample, and the conditions of acquisition: in some experimental conditions combining GC and simple oil-related samples, an EIC of a low abundance species can be as short as 3 to 5 scans.…”

Recent Advances in Petroleum Analysis by Mass Spectrometry

“…Despite the improved coverage of the sample and improved S/N, the authors emphasized that mass spectral segmentation is time-consuming and it may be only suited for targeted analysis. In another report, Gavard et al introduced a batch processing algorithm, Themis, to advance the analysis of replicate complex data sets, such as those measured for petroleum samples . An additional benefit of the algorithm, although not the primary focus, was improved differentiation of genuine signals from noise on the basis of consistency of peak positions across replicates, rather than use of a signal-to-noise threshold alone.…”

Method Considerations for Compound Identification in Complex Mixtures Using Electrospray Ionization Ultrahigh Resolution Mass Spectrometry

“…MF assignment software, such as Composer64 (Sierra Analytics), have various methods for assigning MF to ultrahigh resolution mass spectra and reducing ambiguity (Stanz 2015, Gavard et al 2017. Composer64 reduces ambiguity by selecting the most hydrocarbon-like MF, although the parameters for MF assignment are relatively flexible and customizable.…”