The archived content linked to here is for reference only and may not meet current accessibility standards.
Yu C., Trnka M. J., Baker P. R., Chalkley R. J., Burlingame A., Huang L., Benchmarking MS2- and MS3-based acquisition strategies for XL-MS using a developmental ProteinProspector/Touchstone pipeline 71st ASMS Conference of Mass Spectrometry and Allied Topics, Houston, Texas Jun 4th - Jun 8th 2023
Chalkley R. J., Baker P. R., Glycan Scoring Incorporated into Protein Prospector Database Search Results 70th ASMS Conference of Mass Spectrometry and Allied Topics, Minneapolis, Minnesota Jun 5th - Jun 9th 2022 (pdf)
Baker P. R., Yu C., Chalkley R. J., Integrating Filtered Peak Lists into Protein Prospector's Batch-Tag, 69th ASMS Conference of Mass Spectrometry and Allied Topics, Philadelphia, Pennsylvania Oct 31st - Nov 4th 2021 (pdf)
Chalkley R. J., Baker P. R., Increasing Glycopeptide Identifications through Targeted Y Ion Detection using MS-Filter, 69th ASMS Conference of Mass Spectrometry and Allied Topics, Philadelphia, Pennsylvania Oct 31st - Nov 4th 2021 (pdf)
Yu C., Trnka M., Baker P., Jiao F., Chalkley R. J., Burlingame A., Huang L., Benchmarking fragmentation strategies to maximize cross-linked peptide identification using sulfoxide-containing MS-cleavable reagents, 69th ASMS Conference of Mass Spectrometry and Allied Topics, Philadelphia, Pennsylvania Oct 31st - Nov 4th 2021
Baker P. R., Oses J. A., Gao B., Chalkley R. J., Search Compare Cache Files and the Raw Data Extraction Daemon Improve Quantification Analysis Support and Ease of Protein Prospector Installation, 68th ASMS Conference of Mass Spectrometry and Allied Topics, Online Meeting, June 1st - Jun 12th 2020 (pdf)
Chalkley R. J., Medzihradszky K. F., Darula Z. Pap A., Baker P. R., Complementarity of EThcD and HCD of Glycopeptides: Y ion Filtering for Increased Glycopeptide Identification, 68th ASMS Conference of Mass Spectrometry and Allied Topics, Online Meeting, June 1st - Jun 12th 2020 (pdf)
Binz P.-A., Shofstahl J., Vizcaíno J. A., Barsnes H., Chalkley R. J , Menschaert G., Alpi E., Clauser K., Eng J. K., Lane L., Seymour S. L., Mayer G., Eisenacher M., Perez-Riverol Y., Kapp E. A., Sun Z., Mendoza L., Baker P. R., Deutsch E. W., The PSI Extended FASTA Format (PEFF). 67th ASMS Conference of Mass Spectrometry and Allied Topics, Atlanta, Georgia June 2nd - Jun 6th 2019 (pdf)
Medzihradszky K. F., Baker P. R., Pap A., Darula Z., Chalkley R. J., Expanding the glycoforms detected in complex glycopeptide datasets. 67th ASMS Conference of Mass Spectrometry and Allied Topics, Atlanta, Georgia June 2nd - Jun 6th 2019 (pdf)
Chalkley R. J. and Baker P. R., Augmenting Protein Database Searching with Peptide Library Searching. 66th ASMS Conference of Mass Spectrometry and Allied Topics, San Diego, California June 3rd - Jun 7th 2018 (pdf)
Baker P. R., Knudsen G. M., Yamana A. S., Mendoza L., Moritz R. M. and Chalkley R. J., Integrating Protein Prospector into the Trans-Proteomic Pipeline. 66th ASMS Conference of Mass Spectrometry and Allied Topics, San Diego, California June 3rd - Jun 7th 2018 (pdf)
Chalkley R. J. and Baker P. R., Sharing Annotated Spectra when Standard Formats are not an Option. 16th Human Proteome Organization World Congress, Dublin, Ireland September 17th - September 21st 2017 (pdf)
Baker P. R. and Chalkley R. J., Improvements to Protein Prospector's MS-Viewer. 65th ASMS Conference of Mass Spectrometry and Allied Topics, Indianapolis, Indiana June 4th - Jun 8th 2017 (pdf)
Chalkley R. J. and Baker P. R., Recycling Modification Site Information for Improved Glycopeptide Analysis. 64th ASMS Conference of Mass Spectrometry and Allied Topics, San Antonio, Texas June 5th - Jun 9th 2016 (pdf)
Baker P. R., Oses J. A. and Chalkley R. J., The Benefits of Recycling - Protein Prospector: the Eco-Friendly Search Engine. 64th ASMS Conference of Mass Spectrometry and Allied Topics, San Antonio, Texas June 5th - Jun 9th 2016 (pdf)
Baker P. R. and Chalkley R. J., Additional Variable Modification Search Options in Protein Prospector. 63nd ASMS Conference of Mass Spectrometry and Allied Topics, St. Louis, Missouri May 31st - Jun 4th 2015 (pdf)
Chalkley R. J., Xu S., Baker P. R. and Medzihradszky K. F., Glycopeptidomics: Characterizing Global Glycoprotein and Site Heterogeneity. 63nd ASMS Conference of Mass Spectrometry and Allied Topics, St. Louis, Missouri May 31st - Jun 4th 2015 (pdf)
Chalkley R. J., Trnka M. J., Michael N. and Baker P. R. Identifying Cross-linked Peptides using Protein Prospector. 62nd ASMS Conference of Mass Spectrometry and Allied Topics, Baltimore, Maryland Jun 15th - Jun 19th 2014 (pdf)
Baker P. R., Urisman, A. and Chalkley R. J., Protein Prospector as a Component in a Label-Free/SRM Pipeline. 62nd ASMS Conference of Mass Spectrometry and Allied Topics, Baltimore, Maryland Jun 15th - Jun 19th 2014 (pdf)
Baker P. R., Burlingame A. L. and Chalkley R. J., Importing Data from Different Results Formats into MS-Viewer. 61st ASMS Conference of Mass Spectrometry and Allied Topics, Minneapolis, Minnesota Jun 9th - Jun 13th 2013 (pdf)
Baker P. R., Burlingame A. L. and Chalkley R. J., MS-Viewer - A Web Based Spectral Viewer For Database Search Results. 60th ASMS Conference of Mass Spectrometry and Allied Topics, Vancouver, Canada May 20th - May 24th 2012 (pdf)
Baker P. R., Burlingame A. L. and Chalkley R. J., MS-Viewer - A Web Based Spectral Viewer For Database Search Results. Joint Conference of Polish Mass Spectrometry Society and German Mass Spectrometry Society, Poznan, Poland March 4th - March 7th 2012 (ppt)
Baker P. R., Trinidad J. C., Medzihradszky K. F., Burlingame A. L. and Chalkley R. J., Modification Site Localization Scoring Integrated into a Search Engine. 59th ASMS Conference of Mass Spectrometry and Allied Topics, Denver, Colorado June 5th - June 9th 2011 (pdf)
Baker P. R., Agard N. J., Burlingame A. L. and Chalkley R. J., Quantitative Analysis on the Public Protein Prospector Web Site. 58th ASMS Conference of Mass Spectrometry and Allied Topics, Salt Lake City, Utah May 23rd - May 27th 2010 (pdf)
Chalkley R. J., Baker P. R., Medzihradszky K. F. and Burlingame A. L., Implementation of a Charge-State and Sequence-Dependent Scoring System Dramatically Improves Matching of Peptide ETD Spectra. 58th ASMS Conference of Mass Spectrometry and Allied Topics, Salt Lake City, Utah May 23rd - May 27th 2010 (pdf)
Medzihradszky K. F., Lynn A. J., Chalkley R. J., Baker P. R., Darula Z. and Burlingame A. L., Structural characterization of glycopeptides: Integration of complementary CID and ETD based information. 58th ASMS Conference of Mass Spectrometry and Allied Topics, Salt Lake City, Utah May 23rd - May 27th 2010 (pdf)
Trinidad J. C., Thalhammer A., Lynn A. J., Baker P. R., Schoepfer R. and Burlingame A. L., Activity Dependent Changes in Synaptic Composition 58th ASMS Conference of Mass Spectrometry and Allied Topics, Salt Lake City, Utah May 23rd - May 27th 2010 (pdf)
Trnka M. and Burlingame A. L., Selective Enrichment of Cross-linked Peptides by a Reductive Amination and Click Chemistry Based Cross-linking Strategy. 58th ASMS Conference of Mass Spectrometry and Allied Topics, Salt Lake City, Utah May 23rd - May 27th 2010 (pdf)
Baker P. R., Chalkley R. J., Lynn A. J., Guan S. and Burlingame A. L., Database Searching of Combined ETD and CID Data Using Protein Prospector, 57th ASMS Conference of Mass Spectrometry and Allied Topics, Philadelphia, Pennsylvania May 31st - June 4th 2009 (pdf)
Chalkley R. J., Thalhammer A. J., Schoepfer R. and Burlingame A. L., A Quantum Increase in O-GlcNAc Modification Site Identification Using ETD Analysis on a LTQ Orbitrap, 57th ASMS Conference of Mass Spectrometry and Allied Topics, Philadelphia, Pennsylvania May 31st - June 4th 2009
Eliuk S. M, Maltby D. A., Chalkley R. J., Baker P. R., Panning B. and Burlingame A. L., Elucidating Histone PTM Cross-Talk by Quantitative Mass Spectrometry, 57th ASMS Conference of Mass Spectrometry and Allied Topics, Philadelphia, Pennsylvania May 31st - June 4th 2009
Baker P. R., Chalkley R. J., Medzihradszky K. F. and Burlingame A. L., Comprehensive Analysis of a Published Dataset: Identifying more of your data using the latest Protein Prospector, 56th ASMS Conference of Mass Spectrometry and Allied Topics, Denver, Colorado June 1st - June 5th 2008 (pdf)
Baker P. R., Chalkley R. J., Wang X., Jen N. and Huang L., SILAC and iTRAQ Quantitation on an Orbitrap Using Protein Prospector, 56th ASMS Conference of Mass Spectrometry and Allied Topics, Denver, Colorado June 1st - June 5th 2008 (pdf)
Trinidad J. C., Thalhammer A. Lynn A. J., Baker P. R., Schoepfer R. and Burlingame A. L., Protein and Phosphorylation Expression at the Synapse, 56th ASMS Conference of Mass Spectrometry and Allied Topics, Denver, Colorado June 1st - June 5th 2008
Lynn A. J., Chalkley R. J., Baker P. R., Medzihradszky K. F., Guan S. and Burlingame A. L., The Effect of Peaklist Generation Software on Database Search Results, 56th ASMS Conference of Mass Spectrometry and Allied Topics, Denver, Colorado June 1st - June 5th 2008 (pdf)
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 7th 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 7th 2007 (pdf)
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 7th 2007 (pdf)
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 1st 2006 (pdf)
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 (pdf)
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 (pdf)
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 (pdf)
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 (pdf)
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 (pdf)
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 (pdf)
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 (pdf)
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 (pdf)
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 (pdf)
Huang L., Jacob R. J., Pegg S. C. H., Baldwin M. A. Babbitt P. C. and Burlingame A. L., Identification of Unknown Proteins Through Mining Distant Protein Homology With Mass Spectral Information, 48th ASMS Conference of Mass Spectrometry and Allied Topics, Long Beach, California May 27th - May 31st 2000 (pdf)
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 (click here)
Clauser K. R., Tang C., Rosenberg S., Baker P. R. and Hsieh F., Automated Protein Identification by MALDI-MS. 46th ASMS Conference of Mass Spectrometry and Allied Topics, Orlando, Florida May 30th - June 4th 1998 (click here)
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 (click here)
Clauser K. R., Foulk R. A., Russell A., Baker P. R. Fisher S. J. and Burlingame, A. L., MALDI/PSD Peptide Fragment-Ion Tagging and Mass Fingerprinting of Placental Proteins from 2D Page. 44th ASMS Conference of Mass Spectrometry and Allied Topics, Seattle, Washington May 28th - June 1st 1996 (click here)
.