Lynn A. J., Baker P. R., Chalkley R. J. and Burlingame A. L., Comparison of Database Search Engine Expectation Values, 55th ASMS Conference of Mass Spectrometry and Allied Topics, Indianapolis, Indiana June 3rd - June 7 2007

Baker P. R., Chalkley R. J., Medzihradszky K. F. and Burlingame A. L., Discovery of Unanticipated Modifications using Protein Prospector, 55th ASMS Conference of Mass Spectrometry and Allied Topics, Indianapolis, Indiana June 3rd - June 7 2007

Baker P. R., Chalkley R. J., Trinidad J. C. and Burlingame A. L., New Protein Level Quantitation Features in Protein Prospector, 55th ASMS Conference of Mass Spectrometry and Allied Topics, Indianapolis, Indiana June 3rd - June 7 2007

Wang X., Chen C., Baker P. R. Chen P., Kaiser P and Huang L., Mass Spectrometric of the Affinity-Purified Human 26S Proteasome Complex, Biochemistry, Vol. 46, No. 11, Pp. 3553-3565 (2007)

Hirsch J., Hansen K., Frank J. A., Chalkley R., Fang X., Trinidad J., Baker P., Burlingame A. L., Matthay M., Impact of low and high tidal volume on the rat alveolar epithelial type II cell proteome, Am J Respir Crit Care Med, Vol. 175, No. 10, Pp. 1006-1013 (2007)

Lynn A. J., Chalkley R. J., Baker P. R., Segal M. R. and Burlingame A. L., Protein Prospector and Ways of Calculating Expectation Values, 54th ASMS Conference of Mass Spectrometry and Allied Topics, Seattle, Washington May 28th - June 1 2006

Baker P. R., Medzihradszky K. F. and Burlingame A. L., Improved Methods for Comprehensive Sample Analysis Using Protein Prospector, 54th ASMS Conference of Mass Spectrometry and Allied Topics, Seattle, Washington May 28th - June 1st 2006

Baker P. R., Chalkley R. J., Trinidad J. and Burlingame A. L., Some Recent Enhancements to Protein Prospector, 53rd ASMS Conference of Mass Spectrometry and Allied Topics, San Antonio, Texas June 5th - June 9th 2005

Lynn A. J., Baker P. R., Chang, Y., Chalkley R. J.and Burlingame A. L., Protein Prospector as a Large Scale MS Proteomics Data Management Tool, 53rd ASMS Conference of Mass Spectrometry and Allied Topics, San Antonio, Texas June 5th - June 9th 2005

Chalkley R. J., Baker P. R., Hansen K. C., Medzihradszky K. F., Allen N. P., Rexach M. and Burlingame A. L., Comprehensive Analysis of a Multidimensional Liquid Chromatography Mass Spectrometry Dataset Acquired on a Quadrupole Selecting Quadrupole Collision Cell, Time-of-flight Mass Spectrometer. I. How Much of the Data is Theoretically Interpretable by Search Engines?, Molecular and Cellular Proteomics, Vol. 4, No. 8, Pp. 1189-1193 (2005)

Chalkley R. J., Baker P. R., Huang, L., Hansen K. C., Allen N. P., Rexach M. and Burlingame A. L., Comprehensive Analysis of a Multidimensional Liquid Chromatography Mass Spectrometry Dataset Acquired on a Quadrupole Selecting Quadrupole Collision Cell, Time-of-flight Mass Spectrometer. II. New Developments in Protein Prospector Allow for Reliable and Comprehensive Automatic Analysis of Large Datasets, Molecular and Cellular Proteomics, Vol. 4, No. 8, Pp. 1194-1204 (2005)

Chalkley, R.J., Hansen, K.C. and Baldwin, M.A. Bioinformatic methods to exploit mass spectrometric data for proteomics applications, Methods in Enzymology, Vol. 402, Pp. 289-312 (2005)

Baker P. R., Chalkley R. J., Hansen K. C., Cutillas P. R., Huang, L., Baldwin, M. A. and Burlingame A. L., A Novel Protein Quantitation Algorithm within Protein Prospector, 52nd ASMS Conference of Mass Spectrometry and Allied Topics, Nashville, Tennessee May 23rd - May 27th 2004

Chalkley R. J., Baker P. R., Hansen K. C., Medzihradszky K. F., Allan, N. P., Huang, L., Baldwin, M. A., Rexach, M. and Burlingame A. L., How Much of a Multi-Dimensional LC-MSMS Experiment Acquired on a QSTAR is Interpretable and How Do Database Search Programs Perform, 52nd ASMS Conference of Mass Spectrometry and Allied Topics, Nashville, Tennessee May 23rd - May 27th 2004

Huang, L., Baker P. R., Chalkley R. J., Allan, N. P., Hansen K. C., Rexach, M. and Burlingame A. L., Integrated and Automated Data Processing System for Protein Identification, Characterization and Quantitation, 51st ASMS Conference of Mass Spectrometry and Allied Topics, Montreal, Canada June 8th - June 12th 2003

Chu, F., Baker P., Mahrus, S., Craik, C. S., Rosser, M., Nicchitta, C. V., and Burlingame A. L., Probing Protein-Protein Interactions with Chemical Cross-linking and Differential Nano-LC-MS, 50th ASMS Conference of Mass Spectrometry and Allied Topics, Orlando, Florida June 2nd - June 6th 2002

Huang, L., Chalkley R. J., Baker P. R., Maltby, D., Allan, N. P., Sihlbom, C., Rexach, M., Baldwin, M. A. and Burlingame A. L., High Throughput Proteomic Analysis of Proteins Separated by Gel Electrophoresis Using MALDI TOF/TOF MS and Automated Data Processing, 50th ASMS Conference of Mass Spectrometry and Allied Topics, Orlando, Florida June 2nd - June 6th 2002

Jacob, R. J., Baker P. R., Baldwin, M. A., Graber A. and Burlingame A. L., High Throughput Analysis of MALDI Time-of-flight MS/MS and LCMS/MS Data, 49th ASMS Conference of Mass Spectrometry and Allied Topics, Chicago, Illinois May 27th - May 31st 2001

Jacob, R. J., Baker P. R., Huang, L., Baldwin M. A. and Burlingame A. L., Maximinizing Proteomic Information from MS Data: Enhancements to Protein Prospector, a Suite of Programs for Mining Genomic Databases, 48th ASMS Conference of Mass Spectrometry and Allied Topics, Long Beach, California May 27th - May 31st 2000

Jacob, R. J., Baker P. R., Huang, L., Baldwin M. A. and Burlingame A. L., Maximizing Proteomic Information from MS Data: Enhancements to Protein Prospector, a Suite of Programs for Mining Genomic Databases, 48th ASMS Conference of Mass Spectrometry and Allied Topics, Long Beach, California May 27th - May 31st 2000

Clauser K. R., Baker P. R. and Burlingame A. L., Role of accurate mass measurement (+/- 10 ppm) in protein identification strategies employing MS or MS/MS and database searching. Analytical Chemistry, Vol. 71, No. 14, Pp. 2871-2882 (1999)

Whittal, R., Huang, L., Laiko, V., Clauser K. R., Baker P. R., Baldwin, M. A. and Burlingame, A. L., High mass accuracy peptide mapping using electrospray ionization time-of-flight mass spectrometry with nozzle voltage fragmentation and database searching using MS Tag and MS Fit. 46th ASMS Conference of Mass Spectrometry and Allied Topics, Orlando, Florida May 30th - June 4th 1998

Clauser K. R., Baker P. R. and Burlingame, A. L., Peptide Fragment-Ion Tags from MALDI/PSD for Error-Tolerant Searching of Genomic Databases. 44th ASMS Conference of Mass Spectrometry and Allied Topics, Seattle, Washington May 28th - June 1st 1996