MS Algorithms and Software

XIC Extraction

Massifquant is an open-source solution for KF IT detection that has been subjected to novel and rigorous methods of performance evaluation. The presented evaluation with accompanying annotations and optimization guide sets a new standard for comparative IT detection. Compared with centWave, matchedFilter and MZMine2—alternative IT detection engines—Massifquant detected more true ITs in a real LC-MS complex sample, especially low-intensity ITs. It also offers competitive specificity and equally effective quantitation accuracy. Publication.

Data Storage / Retrieval / Display

MzTree is a spatial database designed to provide real-time storage and retrieval of dynamically summarized standard and augmented MS data with fast performance in both m/z and RT directions. Performance is reported on real data with comparisons against related published retrieval systems. Publication.

JS-MS is a 3-D, modular JavaScript client application for viewing MS data. JS-MS provides several advantages over existing MS viewers, such as a dependency-free, browser-based, one click, cross-platform install and better navigation interfaces. The client includes a modular Java backend with a novel streaming.mzML parser to demonstrate the API-based serving of MS data to the viewer. Publication.

MSabundanceSIM is novel software for simulating any number of molecular samples based on one or a few real world data sets. The software uses a probabilistic model to generate case and control populations, with intuitive user parameters for tuning. We demonstrate variability by comparing to a real world data set over a range of abundances with differing biological and experimental variation coefficients. MSabundanceSIM is implemented in Ruby, is freely available, requires no external dependencies, and is suitable for a range of applications. Publication.


Statistical agglomeration is a novel peak summarization algorithm for direct injection mass spectrometry data that outperforms commercial and ad-hoc methods as measured by peakwise error and pointwise m/z error. Publication.

Rubabel is an intuitive, object-oriented suite of functionality that substantially increases the accessibily of the tools in the Open Babel chemoinformatics library. Rubabel requires fewer lines of code than any other actively developed wrapper, providing better object organization and navigation, and more intuitive object behavior than extant solutions. Moreover, Rubabel provides a convenient interface to the many extensions currently available in Ruby, greatly streamlining otherwise onerous tasks such as creating web applications that serve up Rubabel functionality. Publication.