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Massifquant: open-source Kalman filter-based XC-MS isotope trace feature detection

Christopher J. Conley, Rob Smith, Ralf J. O. Torgrip, Ryan M. Taylor, Ralf Tautenhahn, John T. Prince
2014 Computer applications in the biosciences : CABIOS  
Motivation: Isotope trace (IT) detection is a fundamental step for liquid or gas chromatography mass spectrometry (XC-MS) data analysis that faces a multitude of technical challenges on complex samples  ...  Results: Massifquant is an open-source solution for KF IT detection that has been subjected to novel and rigorous methods of performance evaluation.  ...  DISCUSSION AND CONCLUSIONS In Massifquant, we have implemented an open-source KF-based IT detection algorithm based on Aberg et al. (2008) .  ... 
doi:10.1093/bioinformatics/btu359 pmid:24872423 fatcat:aane7raoufcjpbenwdqevv52c4

Annotated Chromatographic Isotope Features from a Highly Complex Mass Spectrometry Proteomic Dataset (MOUSE) for Feature Detection Algorithm Evaluation

John Prince, Christoper Conley
2013 unpublished
This data set and accompanying annotations, referred to as the MOUSE data set, were used for feature detection algorithm evaluation (FDAE) as described in "Massifquant: open-source Kalman filter based  ...  XC-MS feature detection".  ... 
fatcat:qmvcz4avhbb7rnhbpxcjujyjze

Elucidation and Improvement of Algorithms for Mass Spectrometry Isotope Trace Detection Elucidation and Improvement of Algorithms for Mass Spectrometry Isotope Trace Detection Elucidation and Improvement of Algorithms for Mass Spectrometry Isotope Trace Detection

Robert Smith, Rob Smith, Dan Ventura, John Prince, Mark Clement, Sean Warnick, Bill Barrett, Rob Smith
2014 unpublished
: open-source Kalman filter based XC-MS isotope trace feature detection, Bioinformatics, 2014 We adopt the MS-omics terminology specified in [95]  ...  Discussion & Conclusions In Massifquant, we have implemented an open-source Kalman filter-based IT detection algorithm based on Aberg et al. [1] .  ... 
fatcat:od6n2lzshvdl5ning6ik37zulq

Bioinformatic Solutions to Complex Problems in Mass Spectrometry Based Analysis of Biomolecules BYU ScholarsArchive Citation Bioinformatic Solutions to Complex Problems in Mass Spectrometry Based Analysis of Biomolecules Bioinformatic Solutions to Complex Problems in Mass Spectrometry Based Analysis of Biomolecules

Ryan Taylor, Ryan Taylor, Ryan Taylor, Steven Graves, Barry Willardson, Dixon Woodbury, Ryan Taylor
2014 unpublished
lipid fragmentation prediction tool, introduces custom structural analysis approaches and validation techniques, simplifies protein analysis form SDS-PAGE sample excisions, and implements a robust peak detection  ...  These contributions provide improved identification of biomolecules, improved quantitation, and improve data quality and algorithm clarity to the MS-omic field.  ...  We would like to thank Aman Makaju and Andrew Mathis for assistance in running MS samples. We thank Nathan Doyle for SNAP25B protein production and MS sample preparation.  ... 
fatcat:hqozbx3r3fcttikk6hu3e2eley