Estimating Probabilities of Peptide Assignments to LC-FTICR-MS Observations. - Kevin K. Anderson; Matthew E. Monroe; Don Simone Daly (METMBS, 2004)

VIPER: an advanced software package to support high-throughput LC-MS peptide identification. - Matthew E. Monroe; Nikola Tolic; Navdeep Jaitly; Jason L. Shaw; Joshua N. Adkins; Richard D. Smith (Bioinform., 2007)

DeconMSn: a software tool for accurate parent ion monoisotopic mass determination for tandem mass spectra. - Anoop M. Mayampurath; Navdeep Jaitly; Samuel O. Purvine; Matthew E. Monroe; Kenneth J. Auberry; Joshua N. Adkins; Richard D. Smith (Bioinform., 2008)

MASIC: A software program for fast quantitation and flexible visualization of chromatographic profiles from detected LC-MS(/MS) features. - Matthew E. Monroe; Jason L. Shaw; Don Simone Daly; Joshua N. Adkins; Richard D. Smith (Comput. Biol. Chem., 2008)

An Architecture for Real Time Data Acquisition and Online Signal Processing for High Throughput Tandem Mass Spectrometry. - Anuj R. Shah; Navdeep Jaitly; Nino Zuljevic; Matthew E. Monroe; Andrei Liyu; Ashoka D. Polpitiya; Joshua N. Adkins; Mikhail E. Belov; Gordon A. Anderson; Richard D. Smith; Ian Gorton (eScience, 2009)

Applications in Data-Intensive Computing. - Anuj R. Shah; Joshua N. Adkins; Douglas J. Baxter; William R. Cannon; Daniel G. Chavarría-Miranda; Sutanay Choudhury; Ian Gorton; Deborah K. Gracio; Todd D. Halter; Navdeep Jaitly; John R. Johnson; Richard T. Kouzes; et al. (Adv. Comput., 2010)

Machine learning based prediction for peptide drift times in ion mobility spectrometry. - Anuj R. Shah; Khushbu Agarwal; Erin S. Baker; Mudita Singhal; Anoop M. Mayampurath; Yehia M. Ibrahim; Lars J. Kangas; Matthew E. Monroe; Rui Zhao; Mikhail E. Belov; Gordon A. Anderson; Richard D. Smith (Bioinform., 2010)

Dynamic proteomic profiling of a unicellular cyanobacterium Cyanothece ATCC51142 across light-dark diurnal cycles. - Uma K. Aryal; Jana Stöckel; Ravi K. Krovvidi; Marina A. Gritsenko; Matthew E. Monroe; Ronald J. Moore; David W. Koppenaal; Richard D. Smith; Himadri B. Pakrasi; Jon M. Jacobs (BMC Syst. Biol., 2011)

Toward More Transparent and Reproducible Omics Studies Through a Common Metadata Checklist and Data Publications. - Eugene Kolker; Vural Özdemir; Lennart Martens; William Hancock; Gordon A. Anderson; Nathaniel Anderson; Sukru Aynacioglu; Ancha V. Baranova; Shawn R. Campagna; Rui Chen; John Choiniere; Stephen P. Dearth; et al. (Big Data, 2013)

LC-IMS-MS Feature Finder: detecting multidimensional liquid chromatography, ion mobility and mass spectrometry features in complex datasets. - Kevin L. Crowell; Gordon W. Slysz; Erin S. Baker; Brian L. LaMarche; Matthew E. Monroe; Yehia M. Ibrahim; Samuel H. Payne; Gordon A. Anderson; Richard D. Smith (Bioinform., 2013)

MultiAlign: a multiple LC-MS analysis tool for targeted omics analysis. - Brian L. LaMarche; Kevin L. Crowell; Navdeep Jaitly; Vladislav A. Petyuk; Anuj R. Shah; Ashoka D. Polpitiya; John D. Sandoval; Gary R. Kiebel; Matthew E. Monroe; Stephen J. Callister; Thomas O. Metz; Gordon A. Anderson; et al. (BMC Bioinform., 2013)

Basophile: Accurate Fragment Charge State Prediction Improves Peptide Identification Rates. - Dong Wang; Surendra Dasari; Matthew Chambers; Jerry D. Holman; Kan Chen; Daniel C. Liebler; Daniel J. Orton; Samuel O. Purvine; Matthew E. Monroe; Chang Y. Chung; Kristie L. Rose; David L. Tabb (Genom. Proteom. Bioinform., 2013)

Correcting systematic bias and instrument measurement drift with mzRefinery. - Bryson C. Gibbons; Matthew Chambers; Matthew E. Monroe; David L. Tabb; Samuel H. Payne (Bioinform., 2015)

PIXiE: an algorithm for automated ion mobility arrival time extraction and collision cross section calculation using global data association. - Jian Ma; Cameron P. Casey; Xueyun Zheng; Yehia M. Ibrahim; Christopher S. Wilkins; Ryan S. Renslow; Dennis G. Thomas; Samuel H. Payne; Matthew E. Monroe; Richard D. Smith; Justin G. Teeguarden; Erin S. Baker; et al. (Bioinform., 2017)

Lipid Mini-On: mining and ontology tool for enrichment analysis of lipidomic data. - Geremy Clair; Sarah Reehl; Kelly G. Stratton; Matthew E. Monroe; Malak M. Tfaily; Charles Ansong; Jennifer E. Kyle (Bioinform., 2019)