Protein Prospector Publications
2016

Chalkley R. J. and Baker P. R., Use of a glycosylation site database to improve glycopeptide identification from complex mixtures. Analytical and Bioanalytical Chemistry, doi:10.1007/s00216-016-9981-2 (2016) (link)

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)

Shah A. K., Le Cao K. A., Choi E., Chen D., Gautier B., Nancarrow D., Whiteman D. C., Baker P. R., Clauser K. R., Chalkley R. J., Saunders N. A., Barbour A. P., Joshi V., Hill M. M., Glyco-centric Lectin Magnetic Bead Array (LeMBA) - Proteomics Dataset of Human Serum Samples from Healthy, Barrett's Esophagus and Esophageal Adenocarcinoma Individuals. Data in Brief, Vol. 7, Pp. 1058-1062 (2016) (pdf)

2015

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)

2014

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. and Chalkley R. J., MS-Viewer: A Web Based Spectral Viewer for Proteomics Results. Molecular and Cellular Proteomics, doi:10.1074/mcp.O113.037200 (pdf)

2013

Trnka M. J., Baker P. R., Robinson P. J. J., Burlingame A. L. and Chalkley R. J., Matching cross-linked peptide spectra: only as good as the worse identification. Molecular and Cellular Proteomics, doi:10.1074/mcp.M113.034009 (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)

2012

Cappadona S, Baker P. R., Cutillas P. R. Heck A. J. R. and van Breukelen B., Current challenges in software solutions for mass spectrometry-based quantitative proteomics. Amino Acids, doi:10.1007/s00726-012-1289-8 (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)

2011

Knudsen G. M. and Chalkley R. J., The Effect of Using an Inappropriate Protein Database for Proteomic Data Analysis PLoS ONE6(6): e20873. doi:10.1371/journal.pone.0020873 (link)

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., Trinidad J. C. and Chalkley R. J., Modification Site Localization Scoring Integrated into a Search Engine. Molecular and Cellular Proteomics, Vol. 10, No. 7, doi: 10.1074/mcp.M111.008078 (2011) (pdf)

2010
Darula Z., Chalkley R. J., Lynn A. J., Baker P. R. and Medzihradszky K. F., Improved identification of O-linked glycopeptides from ETD data with optimized scoring for different charge states and cleavage specificities. Amino Acids, DOI 10.1007/s00726-010-0692-2 (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., Medzihradszky K. F. and Chalkley R. J., Improving software performance for peptide ETD data analysis by implementation of charge-state and sequence-dependent scoring. Molecular and Cellular Proteomics, Vol. 9, No. 9, Pp. 1795-1803 (2010) (click here)

Chu F., Baker P. R., Burlingame A. L. and Chalkley R. J., Finding Chimeras: A bioinformatic strategy for identification of cross-linked peptides, Molecular and Cellular Proteomics, Vol. 9, No. 1, Pp. 25-31 (2010) (click here)

Darula Z., Chalkley R. J., Baker P. R., Burlingame A. L. and Medzihradszky K. F., Mass spectrometric analysis, automated identification and complete annotation of O-linked glycopeptides, European Journal of Mass Spectrometry, Vol. 16, Pp. 421-428 (2010) (click here)

2009

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

2008

Chalkley R. J., Baker P. R., Medzihradszky K. F. Lynn A. J. and Burlingame A. L., In-depth Analysis of Tandem Mass Spectrometry Data from Disparate Instrument Types, Molecular and Cellular Proteomics, Vol. 7, No. 12, Pp. 2386-2398 (2008) (pdf)

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)

Trinidad J. C., Thalhammer A., Specht, C. G., Lynn A. J., Baker P. R., Schoepfer R. and Burlingame A. L., Quantitative Analysis of Synaptic Phosphorylation and Protein Expression, Molecular and Cellular Proteomics, Vol. 7, No. 4, Pp. 684-696 (2008) (pdf)

2007

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)

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) (click here)

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) (click here)

2006

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)

2005

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)

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) (pdf)

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) (pdf)

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) (click here)

2004

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

2003

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)

2002

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)

Huang L., Baldwin M. A., Maltby D. A., Medzihradszky K. F., Baker P. R., Allen N., Rexach M., Edmondson R. D., Campbell J., Juhasz P., Martin S. A., Vestal M. L., and Burlingame A.L., The identification of protein-protein interactions of the nuclear pore complex of Saccharomyces cerevisiae using high throughput matrix-assisted laser desorption ionization time-of-flight tandem mass spectrometry. Molecular and Cellular Proteomics, Vol. 1, No. 6, Pp. 434-450 (2002) (pdf)

2001

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)

Jimenez C. R., Huang L., Qiu Y. and Burlingame A. L., Searching sequence databases over the internet: protein identification using MS-Fit. Current protocols in protein science (ed. John E. Coligan), Chapter 16, Unit 16.5. (click here)

Jimenez C. R., Huang L., Qiu Y. and Burlingame A. L., Searching sequence databases over the internet: protein identification using MS-Tag. Current protocols in protein science (ed. John E. Coligan), Chapter 16, Unit 16.6. (click here)

2000

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)

1999

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) (click here)

1998

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)

Qiu Y., Benet L. Z. and Burlingame A. L., Identification of the Hepatic Protein Targets of Reactive Metabolites of Acetaminophen in Vivo in Mice Using Two-dimensional Gel Electrophoresis and Mass Spectrometry. Journal of Biological Chemistry, Vol. 273, No. 28, Pp. 17940-17953 (1998) (click here)

1997

Clauser K. R., Foulk R. A., Baker P. R., Fisher S. J. and Burlingame, A. L., Mining Genome Databases Via Protein Mass-Spectrometry to Understand the Pregnancy Disorder Preeclampsia. FASEB journal, Vol. 11, No. 9, Pp. 1587-1587 (1997) (click here)

1996

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)