Robert Chalkley, PhD
Professional Researcher
Pharmaceutical Chemistry
School of Pharmacy

Publications (110)

Top publication keywords:
ProteomicsPeptidesAcetylglucosamineChromatography, LiquidSoftwareGlycopeptidesDatabases, ProteinComputational BiologyMass SpectrometrySequence Analysis, ProteinProteomeSpectrometry, Mass, Electrospray IonizationSearch EngineTandem Mass SpectrometryProtein Processing, Post-Translational

• CDK1 and CEP97 cooperatively control centriole length to orchestrate ciliogenesis and developmental patterning.
  Genes & development 2026 Liu Y, Wang Z, Sinha T, Li KH, Chalkley RJ, Herranz-Pérez V, Xie C, Yoder BK, Burlingame AL, Black BL, Reiter JF
• Extracellular matrix proteolysis maintains synapse plasticity during brain development.
  Nature neuroscience 2025 Nakajo H, Cao R, Mula SA, McKetney J, Silva NJ, Li KH, Chalkley RJ, Randolph LK, Shah M, Rose IVL, Kampmann M, Swaney DL, Kirst C, Molofsky AV
• Identification of the peptide Vulnusin, a wound signal that mediates mechanical-injury-induced nociception in Drosophila.
  Neuron 2025 Guo Y, Li T, Tuomivaara ST, Teo CF, Feng S, Chalkley RJ, Zhu R, Cheng T, Li KH, Chen W, Simon A, Jin P, Younger S, Yong AJH, Li K, Li K, Burlingame AL, Jan LY, Jan YN
• Proteomic characterization of type I collagen N-terminal crosslinked peptides.
  Matrix biology plus 2025 Darula Z, McCabe MC, Barrett A, Schmitt LR, Maslanka MD, Saviola AJ, Orgel J, Burlingame A, Staab-Weijnitz CA, Stenmark K, Weaver V, Chalkley RJ, Hansen KC
• Can protein expression be 'solved'?
  Trends in biotechnology 2025 Baranowski C, Martin HG, Oyarzún DA, Spinner A, Desai B, Petzold CJ, Nikolados EM, Jaaks-Kraatz S, Gaber A, Chalkley RJ, Scannell D, Sevey R, Jewett MC, Kelly PJ, DeBenedictis EA

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• Comparative analysis of glycoproteomic software using a tailored glycan database.
  Analytical and bioanalytical chemistry 2025 Hogan RA, Pepi LE, Riley NM, Chalkley RJ
• Improving the Depth and Reliability of Glycopeptide Identification Using Protein Prospector.
  Molecular & cellular proteomics : MCP 2025 Chalkley RJ, Baker PR
• Phosphorylation-driven epichaperome assembly is a regulator of cellular adaptability and proliferation.
  Nature communications 2024 Roychowdhury T, McNutt SW, Pasala C, Nguyen HT, Thornton DT, Sharma S, Botticelli L, Digwal CS, Joshi S, Yang N, Panchal P, Chakrabarty S, Bay S, Markov V, Kwong C, Lisanti J, Chung SY, Ginsberg SD, …
• "Comparative Analysis of Glycoproteomic Software Using a Tailored Glycan Database".
  bioRxiv : the preprint server for biology 2024 Hogan RA, Pepi LE, Riley NM, Chalkley RJ
• Phosphorylation-Driven Epichaperome Assembly: A Critical Regulator of Cellular Adaptability and Proliferation.
  Research square 2024 McNutt SW, Roychowdhury T, Pasala C, Nguyen HT, Thornton DT, Sharma S, Botticelli L, Digwal CS, Joshi S, Yang N, Panchal P, Chakrabarty S, Bay S, Markov V, Kwong C, Lisanti J, Chung SY, Ginsberg SD, …
• Assessing Heterogeneity in the N-Telopeptides of Type I Collagen by Mass Spectrometry.
  bioRxiv : the preprint server for biology 2024 Darula Z, McCabe MC, Barrett A, Schmitt LR, Maslanka MD, Saviola AJ, Orgel J, Burlingame A, Staab-Weijnitz CA, Stenmark K, Weaver V, Chalkley RJ, Hansen KC
• A Legionella toxin exhibits tRNA mimicry and glycosyl transferase activity to target the translation machinery and trigger a ribotoxic stress response.
  Nature cell biology 2023 Subramanian A, Wang L, Moss T, Voorhies M, Sangwan S, Stevenson E, Pulido EH, Kwok S, Chalkley RJ, Li KH, Krogan NJ, Swaney DL, Burlingame AL, Floor SN, Sil A, Walter P, Mukherjee S
• SPINDLY mediates O-fucosylation of hundreds of proteins and sugar-dependent growth in Arabidopsis.
  The Plant cell 2023 Bi Y, Shrestha R, Zhang Z, Hsu CC, Reyes AV, Karunadasa S, Baker PR, Maynard JC, Liu Y, Hakimi A, Lopez-Ferrer D, Hassan T, Chalkley RJ, Xu SL, Wang ZY
• Chemical Genetic Identification of PKC Epsilon Substrates in Mouse Brain.
  Molecular & cellular proteomics : MCP 2023 Dugan MP, Ferguson LB, Hertz NT, Chalkley RJ, Burlingame AL, Shokat KM, Parker PJ, Messing RO
• Capture, Release, and Identification of Newly Synthesized Proteins for Improved Profiling of Functional Translatomes.
  Molecular & cellular proteomics : MCP 2023 Phillips NJ, Vinaithirthan BM, Oses-Prieto JA, Chalkley RJ, Burlingame AL
• Application of Parallel Reaction Monitoring in 15N Labeled Samples for Quantification.
  Frontiers in plant science 2022 Reyes AV, Shrestha R, Baker PR, Chalkley RJ, Xu SL
• TSAFinder: exhaustive tumor-specific antigen detection with RNAseq.
  Bioinformatics (Oxford, England) 2022 Sharpnack MF, Johnson TS, Chalkley R, Han Z, Carbone D, Huang K, He K
• 15N Metabolic Labeling Quantification Workflow in Arabidopsis Using Protein Prospector.
  Frontiers in plant science 2022 Shrestha R, Reyes AV, Baker PR, Wang ZY, Chalkley RJ, Xu SL
• Modulating environmental signals to reveal mechanisms and vulnerabilities of cancer persisters.
  Science advances 2022 Sun X, Bieber JM, Hammerlindl H, Chalkley RJ, Li KH, Burlingame AL, Jacobson MP, Wu LF, Altschuler SJ
• Author Correction: Community evaluation of glycoproteomics informatics solutions reveals high-performance search strategies for serum glycopeptide analysis.
  Nature methods 2022 Kawahara R, Chernykh A, Alagesan K, Bern M, Cao W, Chalkley RJ, Cheng K, Choo MS, Edwards N, Goldman R, Hoffmann M, Hu Y, Huang Y, Kim JY, Kletter D, Liquet B, Liu M, Mechref Y, Meng B, Neelamegham S,…
• Community evaluation of glycoproteomics informatics solutions reveals high-performance search strategies for serum glycopeptide analysis.
  Nature methods 2021 Kawahara R, Chernykh A, Alagesan K, Bern M, Cao W, Chalkley RJ, Cheng K, Choo MS, Edwards N, Goldman R, Hoffmann M, Hu Y, Huang Y, Kim JY, Kletter D, Liquet B, Liu M, Mechref Y, Meng B, Neelamegham S,…
• Methods for Enrichment and Assignment of N-Acetylglucosamine Modification Sites.
  Molecular & cellular proteomics : MCP 2021 Maynard JC, Chalkley RJ
• Proteomic analysis of platelet-rich and platelet-poor plasma.
  Regenerative therapy 2020 Miroshnychenko O, Chalkley RJ, Leib RD, Everts PA, Dragoo JL
• Toward Increased Reliability, Transparency, and Accessibility in Cross-linking Mass Spectrometry.
  Structure (London, England : 1993) 2020 Leitner A, Bonvin AMJJ, Borchers CH, Chalkley RJ, Chamot-Rooke J, Combe CW, Cox J, Dong MQ, Fischer L, Götze M, Gozzo FC, Heck AJR, Hoopmann MR, Huang L, Ishihama Y, Jones AR, Kalisman N, Kohlbacher O…
• Characterization of Prenylated C-terminal Peptides Using a Thiopropyl-based Capture Technique and LC-MS/MS.
  Molecular & cellular proteomics : MCP 2020 Wilkins JA, Kaasik K, Chalkley RJ, Burlingame AL
• The effectiveness of filtering glycopeptide peak list files for Y ions.
  Molecular omics 2020 Chalkley RJ, Medzihradszky KF, Darula Z, Pap A, Baker PR
• A two-step probing method to compare lysine accessibility across macromolecular complex conformations.
  RNA biology 2019 MacRae AJ, Coltri P, Hrabeta-Robinson E, Chalkley RJ, Burlingame AL, Jurica MS
• Proteomics Standards Initiative Extended FASTA Format.
  Journal of proteome research 2019 Binz PA, Shofstahl J, Vizcaíno JA, Barsnes H, Chalkley RJ, Menschaert G, Alpi E, Clauser K, Eng JK, Lane L, Seymour SL, Sánchez LFH, Mayer G, Eisenacher M, Perez-Riverol Y, Kapp EA, Mendoza L, Baker …
• Initial Guidelines for Manuscripts Employing Data-independent Acquisition Mass Spectrometry for Proteomic Analysis.
  Molecular & cellular proteomics : MCP 2019 Chalkley RJ, MacCoss MJ, Jaffe JD, Röst HL
• Expanding the Use of Spectral Libraries in Proteomics.
  Journal of proteome research 2018 Deutsch EW, Perez-Riverol Y, Chalkley RJ, Wilhelm M, Tate S, Sachsenberg T, Walzer M, Käll L, Delanghe B, Böcker S, Schymanski EL, Wilmes P, Dorfer V, Kuster B, Volders PJ, Jehmlich N, Vissers JPC, …
• Prp8 positioning of U5 snRNA is linked to 5' splice site recognition.
  RNA (New York, N.Y.) 2018 MacRae AJ, Mayerle M, Hrabeta-Robinson E, Chalkley RJ, Guthrie C, Burlingame AL, Jurica MS
• Revealing nascent proteomics in signaling pathways and cell differentiation.
  Proceedings of the National Academy of Sciences of the United States of America 2018 Forester CM, Zhao Q, Phillips NJ, Urisman A, Chalkley RJ, Oses-Prieto JA, Zhang L, Ruggero D, Burlingame AL
• Peripheral Elevation of a Klotho Fragment Enhances Brain Function and Resilience in Young, Aging, and α-Synuclein Transgenic Mice.
  Cell reports 2017 Leon J, Moreno AJ, Garay BI, Chalkley RJ, Burlingame AL, Wang D, Dubal DB
• The mzIdentML Data Standard Version 1.2, Supporting Advances in Proteome Informatics.
  Molecular & cellular proteomics : MCP 2017 Vizcaíno JA, Mayer G, Perkins S, Barsnes H, Vaudel M, Perez-Riverol Y, Ternent T, Uszkoreit J, Eisenacher M, Fischer L, Rappsilber J, Netz E, Walzer M, Kohlbacher O, Leitner A, Chalkley RJ, Ghali F, …
• PPKs mediate direct signal transfer from phytochrome photoreceptors to transcription factor PIF3.
  Nature communications 2017 Ni W, Xu SL, González-Grandío E, Chalkley RJ, Huhmer AFR, Burlingame AL, Wang ZY, Quail PH
• Hyper-O-GlcNAcylation activates nuclear factor κ-light-chain-enhancer of activated B cells (NF-κB) signaling through interplay with phosphorylation and acetylation.
  The Journal of biological chemistry 2017 Ma Z, Chalkley RJ, Vosseller K
• New Guidelines for Publication of Manuscripts Describing Development and Application of Targeted Mass Spectrometry Measurements of Peptides and Proteins.
  Molecular & cellular proteomics : MCP 2017 Abbatiello S, Ackermann BL, Borchers C, Bradshaw RA, Carr SA, Chalkley R, Choi M, Deutsch E, Domon B, Hoofnagle AN, Keshishian H, Kuhn E, Liebler DC, MacCoss M, MacLean B, Mani DR, Neubert H, Smith D,…
• Proteomic analysis reveals O-GlcNAc modification on proteins with key regulatory functions in Arabidopsis.
  Proceedings of the National Academy of Sciences of the United States of America 2017 Xu SL, Chalkley RJ, Maynard JC, Wang W, Ni W, Jiang X, Shin K, Cheng L, Savage D, Hühmer AF, Burlingame AL, Wang ZY
• Use of a glycosylation site database to improve glycopeptide identification from complex mixtures.
  Analytical and bioanalytical chemistry 2016 Chalkley RJ, Baker PR
• N-Glycopeptide Profiling in Arabidopsis Inflorescence.
  Molecular & cellular proteomics : MCP 2016 Xu SL, Medzihradszky KF, Wang ZY, Burlingame AL, Chalkley RJ
• 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 2016 Shah AK, Lê Cao KA, Choi E, Chen D, Gautier B, Nancarrow D, Whiteman DC, Baker PR, Clauser KR, Chalkley RJ, Saunders NA, Barbour AP, Joshi V, Hill MM
• Modification Site Localization in Peptides.
  Advances in experimental medicine and biology 2016 Chalkley RJ
• Use of a mutant OGA for detecting O-GlcNAc modified proteins.
  The Biochemical journal 2015 Chalkley RJ
• On Credibility, Clarity, and Compliance.
  Molecular & cellular proteomics : MCP 2015 Burlingame A, Carr SA, Bradshaw RA, Chalkley RJ
• Proteotranscriptomic Profiling of 231-BR Breast Cancer Cells: Identification of Potential Biomarkers and Therapeutic Targets for Brain Metastasis.
  Molecular & cellular proteomics : MCP 2015 Dun MD, Chalkley RJ, Faulkner S, Keene S, Avery-Kiejda KA, Scott RJ, Falkenby LG, Cairns MJ, Larsen MR, Bradshaw RA, Hondermarck H
• Tissue-Specific Glycosylation at the Glycopeptide Level.
  Molecular & cellular proteomics : MCP 2015 Medzihradszky KF, Kaasik K, Chalkley RJ
• Characterizing sialic acid variants at the glycopeptide level.
  Analytical chemistry 2015 Medzihradszky KF, Kaasik K, Chalkley RJ
• Lessons in de novo peptide sequencing by tandem mass spectrometry.
  Mass spectrometry reviews 2015 Medzihradszky KF, Chalkley RJ
• NGF and ProNGF: Regulation of neuronal and neoplastic responses through receptor signaling.
  Advances in biological regulation 2014 Bradshaw RA, Pundavela J, Biarc J, Chalkley RJ, Burlingame AL, Hondermarck H
• A standardized framing for reporting protein identifications in mzIdentML 1.2.
  Proteomics 2014 Seymour SL, Farrah T, Binz PA, Chalkley RJ, Cottrell JS, Searle BC, Tabb DL, Vizcaíno JA, Prieto G, Uszkoreit J, Eisenacher M, Martínez-Bartolomé S, Ghali F, Jones AR
• Molecular architecture of photoreceptor phosphodiesterase elucidated by chemical cross-linking and integrative modeling.
  Journal of molecular biology 2014 Zeng-Elmore X, Gao XZ, Pellarin R, Schneidman-Duhovny D, Zhang XJ, Kozacka KA, Tang Y, Sali A, Chalkley RJ, Cote RH, Chu F
• Double impact of cigarette smoke and mechanical ventilation on the alveolar epithelial type II cell.
  Critical care (London, England) 2014 Hirsch J, Chalkley RJ, Bentley T, Burlingame AL, Frank JA
• MS-viewer: a web-based spectral viewer for proteomics results.
  Molecular & cellular proteomics : MCP 2014 Baker PR, Chalkley RJ
• ProteomeXchange provides globally coordinated proteomics data submission and dissemination.
  Nature biotechnology 2014 Vizcaíno JA, Deutsch EW, Wang R, Csordas A, Reisinger F, Ríos D, Dianes JA, Sun Z, Farrah T, Bandeira N, Binz PA, Xenarios I, Eisenacher M, Mayer G, Gatto L, Campos A, Chalkley RJ, Kraus HJ, Albar JP,…
• Matching cross-linked peptide spectra: only as good as the worse identification.
  Molecular & cellular proteomics : MCP 2013 Trnka MJ, Baker PR, Robinson PJ, Burlingame AL, Chalkley RJ
• O-linked β-N-acetylglucosamine (O-GlcNAc) site thr-87 regulates synapsin I localization to synapses and size of the reserve pool of synaptic vesicles.
  The Journal of biological chemistry 2013 Skorobogatko Y, Landicho A, Chalkley RJ, Kossenkov AV, Gallo G, Vosseller K
• Proteome informatics research group (iPRG)_2012: a study on detecting modified peptides in a complex mixture.
  Molecular & cellular proteomics : MCP 2013 Chalkley RJ, Bandeira N, Chambers MC, Clauser KR, Cottrell JS, Deutsch EW, Kapp EA, Lam HH, McDonald WH, Neubert TA, Sun RX
• Multisite light-induced phosphorylation of the transcription factor PIF3 is necessary for both its rapid degradation and concomitant negative feedback modulation of photoreceptor phyB levels in Arabidopsis.
  The Plant cell 2013 Ni W, Xu SL, Chalkley RJ, Pham TN, Guan S, Maltby DA, Burlingame AL, Wang ZY, Quail PH
• Dissecting the roles of tyrosines 490 and 785 of TrkA protein in the induction of downstream protein phosphorylation using chimeric receptors.
  The Journal of biological chemistry 2013 Biarc J, Chalkley RJ, Burlingame AL, Bradshaw RA
• Glucose sensor O-GlcNAcylation coordinates with phosphorylation to regulate circadian clock.
  Cell metabolism 2013 Kaasik K, Kivimäe S, Allen JJ, Chalkley RJ, Huang Y, Baer K, Kissel H, Burlingame AL, Shokat KM, Ptácek LJ, Fu YH
• Rearrangements within human spliceosomes captured after exon ligation.
  RNA (New York, N.Y.) 2013 Ilagan JO, Chalkley RJ, Burlingame AL, Jurica MS
• When target-decoy false discovery rate estimations are inaccurate and how to spot instances.
  Journal of proteome research 2013 Chalkley RJ
• Improving Peptide identification using empirical scoring systems.
  Methods in molecular biology (Clifton, N.J.) 2013 Chalkley RJ
• The DegraBase: a database of proteolysis in healthy and apoptotic human cells.
  Molecular & cellular proteomics : MCP 2012 Crawford ED, Seaman JE, Agard N, Hsu GW, Julien O, Mahrus S, Nguyen H, Shimbo K, Yoshihara HA, Zhuang M, Chalkley RJ, Wells JA
• Modification site localization scoring: strategies and performance.
  Molecular & cellular proteomics : MCP 2012 Chalkley RJ, Clauser KR
• Identification of O-linked β-D-N-acetylglucosamine-modified proteins from Arabidopsis.
  Methods in molecular biology (Clifton, N.J.) 2012 Xu SL, Chalkley RJ, Wang ZY, Burlingame AL
• The induction of serine/threonine protein phosphorylations by a PDGFR/TrkA chimera in stably transfected PC12 cells.
  Molecular & cellular proteomics : MCP 2011 Biarc J, Chalkley RJ, Burlingame AL, Bradshaw RA
• The effect of using an inappropriate protein database for proteomic data analysis.
  PloS one 2011 Knudsen GM, Chalkley RJ
• Breaking up the C complex spliceosome shows stable association of proteins with the lariat intron intermediate.
  PloS one 2011 Coltri P, Effenberger K, Chalkley RJ, Burlingame AL, Jurica MS
• Modification site localization scoring integrated into a search engine.
  Molecular & cellular proteomics : MCP 2011 Baker PR, Trinidad JC, Chalkley RJ
• Receptor tyrosine kinase signaling--a proteomic perspective.
  Advances in enzyme regulation 2010 Biarc J, Chalkley RJ, Burlingame AL, Bradshaw RA
• Protein PTMs: post-translational modifications or pesky trouble makers?
  Journal of mass spectrometry : JMS 2010 Bradshaw RA, Medzihradszky KF, Chalkley RJ
• Improved identification of O-linked glycopeptides from ETD data with optimized scoring for different charge states and cleavage specificities.
  Amino acids 2010 Darula Z, Chalkley RJ, Lynn A, Baker PR, Medzihradszky KF
• The transcriptional coactivator DRIP/mediator complex is involved in vitamin D receptor function and regulates keratinocyte proliferation and differentiation.
  The Journal of investigative dermatology 2010 Oda Y, Chalkley RJ, Burlingame AL, Bikle DD
• Improving software performance for peptide electron transfer dissociation data analysis by implementation of charge state- and sequence-dependent scoring.
  Molecular & cellular proteomics : MCP 2010 Baker PR, Medzihradszky KF, Chalkley RJ
• Phosphopeptide screen uncovers novel phosphorylation sites of Nedd4-2 that potentiate its inhibition of the epithelial Na+ channel.
  The Journal of biological chemistry 2010 Hallows KR, Bhalla V, Oyster NM, Wijngaarden MA, Lee JK, Li H, Chandran S, Xia X, Huang Z, Chalkley RJ, Burlingame AL, Pearce D
• The RasGAP proteins Ira2 and neurofibromin are negatively regulated by Gpb1 in yeast and ETEA in humans.
  Molecular and cellular biology 2010 Phan VT, Ding VW, Li F, Chalkley RJ, Burlingame A, McCormick F
• Statistical analysis of Peptide electron transfer dissociation fragmentation mass spectrometry.
  Analytical chemistry 2010 Chalkley RJ, Medzihradszky KF, Lynn AJ, Baker PR, Burlingame AL
• Instrumentation for LC-MS/MS in proteomics.
  Methods in molecular biology (Clifton, N.J.) 2010 Chalkley R
• Mass spectrometric analysis, automated identification and complete annotation of O-linked glycopeptides.
  European journal of mass spectrometry (Chichester, England) 2010 Darula Z, Chalkley RJ, Baker P, Burlingame AL, Medzihradszky KF
• Finding chimeras: a bioinformatics strategy for identification of cross-linked peptides.
  Molecular & cellular proteomics : MCP 2009 Chu F, Baker PR, Burlingame AL, Chalkley RJ
• The role of exon sequences in C complex spliceosome structure.
  Journal of molecular biology 2009 Ilagan J, Yuh P, Chalkley RJ, Burlingame AL, Jurica MS
• Recommendations from the 2008 International Summit on Proteomics Data Release and Sharing Policy: the Amsterdam principles.
  Journal of proteome research 2009 Rodriguez H, Snyder M, Uhlén M, Andrews P, Beavis R, Borchers C, Chalkley RJ, Cho SY, Cottingham K, Dunn M, Dylag T, Edgar R, Hare P, Heck AJ, Hirsch RF, Kennedy K, Kolar P, Kraus HJ, Mallick P, …
• Identification of protein O-GlcNAcylation sites using electron transfer dissociation mass spectrometry on native peptides.
  Proceedings of the National Academy of Sciences of the United States of America 2009 Chalkley RJ, Thalhammer A, Schoepfer R, Burlingame AL
• HDL antielastase activity prevents smooth muscle cell anoikis, a potential new antiatherogenic property.
  FASEB journal : official publication of the Federation of American Societies for Experimental Biology 2009 Ortiz-Muñoz G, Houard X, Martín-Ventura JL, Ishida BY, Loyau S, Rossignol P, Moreno JA, Kane JP, Chalkley RJ, Burlingame AL, Michel JB, Meilhac O
• Human antibodies targeting cell surface antigens overexpressed by the hormone refractory metastatic prostate cancer cells: ICAM-1 is a tumor antigen that mediates prostate cancer cell invasion.
  Journal of molecular medicine (Berlin, Germany) 2009 Conrad F, Zhu X, Zhang X, Chalkley RJ, Burlingame AL, Marks JD, Liu B
• Identification of new p53 acetylation sites in COS-1 cells.
  Molecular & cellular proteomics : MCP 2009 Joubel A, Chalkley RJ, Medzihradszky KF, Hondermarck H, Burlingame AL
• The PSI-MOD community standard for representation of protein modification data.
  Nature biotechnology 2008 Montecchi-Palazzi L, Beavis R, Binz PA, Chalkley RJ, Cottrell J, Creasy D, Shofstahl J, Seymour SL, Garavelli JS
• In-depth analysis of tandem mass spectrometry data from disparate instrument types.
  Molecular & cellular proteomics : MCP 2008 Chalkley RJ, Baker PR, Medzihradszky KF, Lynn AJ, Burlingame AL
• Cell cycle-dependent phosphorylation of human CDC5 regulates RNA processing.
  Cell cycle (Georgetown, Tex.) 2008 Gräub R, Lancero H, Pedersen A, Chu M, Padmanabhan K, Xu XQ, Spitz P, Chalkley R, Burlingame AL, Stokoe D, Bernstein HS
• A proteomics study of brassinosteroid response in Arabidopsis.
  Molecular & cellular proteomics : MCP 2007 Deng Z, Zhang X, Tang W, Oses-Prieto JA, Suzuki N, Gendron JM, Chen H, Guan S, Chalkley RJ, Peterman TK, Burlingame AL, Wang ZY
• Impact of low and high tidal volumes on the rat alveolar epithelial type II cell proteome.
  American journal of respiratory and critical care medicine 2007 Hirsch J, Hansen KC, Sapru A, Frank JA, Chalkley RJ, Fang X, Trinidad JC, Baker P, Burlingame AL, Matthay MA
• Side-chain fragmentation of alkylated cysteine residues in electron capture dissociation mass spectrometry.
  Journal of the American Society for Mass Spectrometry 2006 Chalkley RJ, Brinkworth CS, Burlingame AL
• Keratin 20 serine 13 phosphorylation is a stress and intestinal goblet cell marker.
  The Journal of biological chemistry 2006 Zhou Q, Cadrin M, Herrmann H, Chen CH, Chalkley RJ, Burlingame AL, Omary MB
• O-linked N-acetylglucosamine proteomics of postsynaptic density preparations using lectin weak affinity chromatography and mass spectrometry.
  Molecular & cellular proteomics : MCP 2006 Vosseller K, Trinidad JC, Chalkley RJ, Specht CG, Thalhammer A, Lynn AJ, Snedecor JO, Guan S, Medzihradszky KF, Maltby DA, Schoepfer R, Burlingame AL
• Mapping post-translational modifications of the histone variant MacroH2A1 using tandem mass spectrometry.
  Molecular & cellular proteomics : MCP 2005 Chu F, Nusinow DA, Chalkley RJ, Plath K, Panning B, Burlingame AL
• Mass spectrometric analysis of histone posttranslational modifications.
  Methods (San Diego, Calif.) 2005 Burlingame AL, Zhang X, Chalkley RJ
• A combinatorial code for the interaction of alpha-synuclein with membranes.
  The Journal of biological chemistry 2005 Kubo S, Nemani VM, Chalkley RJ, Anthony MD, Hattori N, Mizuno Y, Edwards RH, Fortin DL
• 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 & cellular proteomics : MCP 2005 Chalkley RJ, Baker PR, Huang L, Hansen KC, Allen NP, Rexach M, Burlingame AL
• 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 & cellular proteomics : MCP 2005 Chalkley RJ, Baker PR, Hansen KC, Medzihradszky KF, Allen NP, Rexach M, Burlingame AL
• Quantitative analysis of both protein expression and serine / threonine post-translational modifications through stable isotope labeling with dithiothreitol.
  Proteomics 2005 Vosseller K, Hansen KC, Chalkley RJ, Trinidad JC, Wells L, Hart GW, Burlingame AL
• Bioinformatic methods to exploit mass spectrometric data for proteomic applications.
  Methods in enzymology 2005 Chalkley RJ, Hansen KC, Baldwin MA
• The urinary proteome in Fanconi syndrome implies specificity in the reabsorption of proteins by renal proximal tubule cells.
  American journal of physiology. Renal physiology 2004 Cutillas PR, Chalkley RJ, Hansen KC, Cramer R, Norden AG, Waterfield MD, Burlingame AL, Unwin RJ
• Two distinct coactivators, DRIP/mediator and SRC/p160, are differentially involved in VDR transactivation during keratinocyte differentiation.
  The Journal of steroid biochemistry and molecular biology 2004 Oda Y, Sihlbom C, Chalkley RJ, Huang L, Rachez C, Chang CP, Burlingame AL, Freedman LP, Bikle DD
• Regulated expression of apolipoprotein E by human retinal pigment epithelial cells.
  Journal of lipid research 2003 Ishida BY, Bailey KR, Duncan KG, Chalkley RJ, Burlingame AL, Kane JP, Schwartz DM
• Two distinct coactivators, DRIP/mediator and SRC/p160, are differentially involved in vitamin D receptor transactivation during keratinocyte differentiation.
  Molecular endocrinology (Baltimore, Md.) 2003 Oda Y, Sihlbom C, Chalkley RJ, Huang L, Rachez C, Chang CP, Burlingame AL, Freedman LP, Bikle DD
• Mass spectrometric analysis of protein mixtures at low levels using cleavable 13C-isotope-coded affinity tag and multidimensional chromatography.
  Molecular & cellular proteomics : MCP 2003 Hansen KC, Schmitt-Ulms G, Chalkley RJ, Hirsch J, Baldwin MA, Burlingame AL
• Linking the T cell surface protein CD2 to the actin-capping protein CAPZ via CMS and CIN85.
  The Journal of biological chemistry 2003 Hutchings NJ, Clarkson N, Chalkley R, Barclay AN, Brown MH
• Identification of novel sites of O-N-acetylglucosamine modification of serum response factor using quadrupole time-of-flight mass spectrometry.
  Molecular & cellular proteomics : MCP 2003 Chalkley RJ, Burlingame AL
• Deciphering networks of protein interactions at the nuclear pore complex.
  Molecular & cellular proteomics : MCP 2002 Allen NP, Patel SS, Huang L, Chalkley RJ, Burlingame A, Lutzmann M, Hurt EC, Rexach M