Chalkley RJ, Baker PR, Improving the Depth and Reliability of Glycopeptide Identification Using Protein Prospector, Molecular & Cellular Proteomics (2025), doi: (https://doi.org/10.1016/j.mcpro.2025.100903)
D’Auria, G., Baker, P.R., Nitride, C., Ferranti, P.,(2024) Experimental Design and Data Acquisition in Food Proteomics Using Protein Prospector. In: Ferranti, P. (eds) Proteomics Applied to Foods. Methods and Protocols in Food Science. Humana, New York, NY. (https://doi.org/10.1007/978-1-0716-4075-3_3)
Roychowdhury, T., McNutt, S.W., Pasala, C. Nguyen, H.T,, Thornton, D.T., Sharma, S., Botticelli, L., Chander S. Digwal, Joshi, S., Yang, N., Panchal, P., Chakrabarty, S., Bay, S., Markov, V., Kwong, C., Lisanti, J., Chung, S.Y., Ginsberg, S.D., Yan, P., De Stanchina, E., Corben, A., Modi, S., Alpaugh, M.L., Colombo, G., Erdjument-Bromage, H., Neubert, T.A., Chalkley, R.J., Baker, P.R., Burlingame, A.L., Anna Rodina, Chiosis, G., Chu, F. Phosphorylation-driven epichaperome assembly is a regulator of cellular adaptability and proliferation. Nat Commun 15, 8912 (2024). (https://doi.org/10.1038/s41467-024-53178-5)
Bi Y., Shrestha R., Zhang Z., Hsu C. C., Reyes A. V., Karunadasa S., Baker P. R., Maynard J. C, Liu Y., Hakimi A., Lopez-Ferrer D., Hassan T., Chalkley R J., Xu S-L., Wang Z. Y., SPINDLY mediates O-fucosylation of hundreds of proteins and sugar-dependent growth in Arabidopsis, The Plant Cell, 2023 Feb 6, https://doi.org/10.1093/plcell/koad023 (link)
Shrestha R., Reyes A. V., Baker P. R., Wang Z. Y., Chalkley R. J., Xu S. L., 15N Metabolic Labeling Quantification Workflow in Arabidopsis Using Protein Prospector. Front Plant Sci. 2022: Vol. 13: 832562. https://doi.org/10.3389/fpls.2022.832562 (link)
Reyes A. V., Shrestha R., Baker P. R., Chalkley R. J., Xu S. L., Application of Parallel Reaction Monitoring in 15N Labeled Samples for Quantification. Front Plant Sci. 2022; Vol. 13: 832585. https://doi.org/10.3389/fpls.2022.832585 (link)
Wheat A., Yu C., Wang X., Burke A. M., Chemmama I. E., Kaake R. M., Baker P., Rychnovsky S. D., Yang J., Huang L., Protein interaction landscapes revealed by advanced in vivo cross-linking-mass spectrometry, Proc. Natl. Acad. Sci. USA, Vol. 118, No. 32, e2023360118 (link)
Chalkley R. J., Medzihradszky K. F., Pap A., Darula Z., Baker P. R., The effectiveness of filtering glycopeptide peak list files for Y ions, Molecular Omics, Vol. 16, No 2. Pp. 147-155. (link)
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., Sánchez L. F. H., Mayer G., Eisenacher M., Perez-Riverol Y., Kapp E. A., Mendoza L., Baker P. R., Collins A., Van Den Bossche T., Deutsch E. W., Proteomics Standards Initiative Extended FASTA Format, Journal of Proteomics Research, Vol. 18, No. 6, Pp. 2686-2692, doi: 10.1021/acs.jproteome.9b00064 (2019) (pdf)
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)
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)
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)
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)
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)
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. 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)
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)
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)
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)
Wang X., Chen C., Baker P. R. Chen P., Kaiser P and Huang L., Mass Spectrometric Characterization 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)
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)
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)
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)
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)
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)
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)
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