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Initial Guidelines for Manuscripts Employing Data-independent Acquisition Mass Spectrometry for Proteomic Analysis.

Chalkley RJ, MacCoss MJ, Jaffe JD, Röst HL.

Mol Cell Proteomics. 2019 Jan;18(1):1-2. doi: 10.1074/mcp.E118.001286. No abstract available.


Expanding the use of spectral libraries in proteomics.

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, Wolan DW, Wang AY, Mendoza L, Shofstahl J, Dowsey AW, Griss J, Salek RM, Neumann S, Binz PA, Lam H, Vizcaíno JA, Bandeira N, Röst H.

J Proteome Res. 2018 Oct 1. doi: 10.1021/acs.jproteome.8b00485. [Epub ahead of print]


Prp8 positioning of U5 snRNA is linked to 5' splice site recognition.

MacRae AJ, Mayerle M, Hrabeta-Robinson E, Chalkley RJ, Guthrie C, Burlingame AL, Jurica MS.

RNA. 2018 Jun;24(6):769-777. doi: 10.1261/rna.065458.117. Epub 2018 Feb 27.


Revealing nascent proteomics in signaling pathways and cell differentiation.

Forester CM, Zhao Q, Phillips NJ, Urisman A, Chalkley RJ, Oses-Prieto JA, Zhang L, Ruggero D, Burlingame AL.

Proc Natl Acad Sci U S A. 2018 Mar 6;115(10):2353-2358. doi: 10.1073/pnas.1707514115. Epub 2018 Feb 21.


Peripheral Elevation of a Klotho Fragment Enhances Brain Function and Resilience in Young, Aging, and α-Synuclein Transgenic Mice.

Leon J, Moreno AJ, Garay BI, Chalkley RJ, Burlingame AL, Wang D, Dubal DB.

Cell Rep. 2017 Aug 8;20(6):1360-1371. doi: 10.1016/j.celrep.2017.07.024.


The mzIdentML Data Standard Version 1.2, Supporting Advances in Proteome Informatics.

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, Martínez-Bartolomé S, Deutsch EW, Jones AR.

Mol Cell Proteomics. 2017 Jul;16(7):1275-1285. doi: 10.1074/mcp.M117.068429. Epub 2017 May 17.


PPKs mediate direct signal transfer from phytochrome photoreceptors to transcription factor PIF3.

Ni W, Xu SL, González-Grandío E, Chalkley RJ, Huhmer AFR, Burlingame AL, Wang ZY, Quail PH.

Nat Commun. 2017 May 11;8:15236. doi: 10.1038/ncomms15236.


Hyper-O-GlcNAcylation activates nuclear factor κ-light-chain-enhancer of activated B cells (NF-κB) signaling through interplay with phosphorylation and acetylation.

Ma Z, Chalkley RJ, Vosseller K.

J Biol Chem. 2017 Jun 2;292(22):9150-9163. doi: 10.1074/jbc.M116.766568. Epub 2017 Apr 17.


Proteomic analysis reveals O-GlcNAc modification on proteins with key regulatory functions in Arabidopsis.

Xu SL, Chalkley RJ, Maynard JC, Wang W, Ni W, Jiang X, Shin K, Cheng L, Savage D, Hühmer AF, Burlingame AL, Wang ZY.

Proc Natl Acad Sci U S A. 2017 Feb 21;114(8):E1536-E1543. doi: 10.1073/pnas.1610452114. Epub 2017 Feb 2.


Modification Site Localization in Peptides.

Chalkley RJ.

Adv Exp Med Biol. 2016;919:243-247. Review.


Use of a glycosylation site database to improve glycopeptide identification from complex mixtures.

Chalkley RJ, Baker PR.

Anal Bioanal Chem. 2017 Jan;409(2):571-577. doi: 10.1007/s00216-016-9981-2. Epub 2016 Oct 8.


Glyco-centric lectin magnetic bead array (LeMBA) - proteomics dataset of human serum samples from healthy, Barrett׳s esophagus and esophageal adenocarcinoma individuals.

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.

Data Brief. 2016 Apr 1;7:1058-62. doi: 10.1016/j.dib.2016.03.081. eCollection 2016 Jun.


N-Glycopeptide Profiling in Arabidopsis Inflorescence.

Xu SL, Medzihradszky KF, Wang ZY, Burlingame AL, Chalkley RJ.

Mol Cell Proteomics. 2016 Jun;15(6):2048-54. doi: 10.1074/mcp.M115.056101. Epub 2016 Apr 11.


Use of a mutant OGA for detecting O-GlcNAc modified proteins.

Chalkley RJ.

Biochem J. 2015 Dec 1;472(2):e25-6. doi: 10.1042/BJ20150970.


Proteotranscriptomic Profiling of 231-BR Breast Cancer Cells: Identification of Potential Biomarkers and Therapeutic Targets for Brain Metastasis.

Dun MD, Chalkley RJ, Faulkner S, Keene S, Avery-Kiejda KA, Scott RJ, Falkenby LG, Cairns MJ, Larsen MR, Bradshaw RA, Hondermarck H.

Mol Cell Proteomics. 2015 Sep;14(9):2316-30. doi: 10.1074/mcp.M114.046110. Epub 2015 Jun 3.


On Credibility, Clarity, and Compliance.

Burlingame A, Carr SA, Bradshaw RA, Chalkley RJ.

Mol Cell Proteomics. 2015 Jul;14(7):1731-3. doi: 10.1074/mcp.E115.052506. Epub 2015 Jun 3. No abstract available.


Tissue-Specific Glycosylation at the Glycopeptide Level.

Medzihradszky KF, Kaasik K, Chalkley RJ.

Mol Cell Proteomics. 2015 Aug;14(8):2103-10. doi: 10.1074/mcp.M115.050393. Epub 2015 May 20.


Lessons in de novo peptide sequencing by tandem mass spectrometry.

Medzihradszky KF, Chalkley RJ.

Mass Spectrom Rev. 2015 Jan-Feb;34(1):43-63. Review.


Characterizing sialic acid variants at the glycopeptide level.

Medzihradszky KF, Kaasik K, Chalkley RJ.

Anal Chem. 2015 Mar 3;87(5):3064-71. doi: 10.1021/ac504725r. Epub 2015 Feb 17.


NGF and ProNGF: Regulation of neuronal and neoplastic responses through receptor signaling.

Bradshaw RA, Pundavela J, Biarc J, Chalkley RJ, Burlingame AL, Hondermarck H.

Adv Biol Regul. 2015 May;58:16-27. doi: 10.1016/j.jbior.2014.11.003. Epub 2014 Nov 20. Review.


Molecular architecture of photoreceptor phosphodiesterase elucidated by chemical cross-linking and integrative modeling.

Zeng-Elmore X, Gao XZ, Pellarin R, Schneidman-Duhovny D, Zhang XJ, Kozacka KA, Tang Y, Sali A, Chalkley RJ, Cote RH, Chu F.

J Mol Biol. 2014 Nov 11;426(22):3713-3728. doi: 10.1016/j.jmb.2014.07.033. Epub 2014 Aug 19.


A standardized framing for reporting protein identifications in mzIdentML 1.2.

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.

Proteomics. 2014 Nov;14(21-22):2389-99. doi: 10.1002/pmic.201400080. Epub 2014 Sep 23.


ProteomeXchange provides globally coordinated proteomics data submission and dissemination.

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, Martinez-Bartolomé S, Apweiler R, Omenn GS, Martens L, Jones AR, Hermjakob H.

Nat Biotechnol. 2014 Mar;32(3):223-6. doi: 10.1038/nbt.2839. No abstract available.


Double impact of cigarette smoke and mechanical ventilation on the alveolar epithelial type II cell.

Hirsch J, Chalkley RJ, Bentley T, Burlingame AL, Frank JA.

Crit Care. 2014 Mar 25;18(2):R50. doi: 10.1186/cc13795.


MS-viewer: a web-based spectral viewer for proteomics results.

Baker PR, Chalkley RJ.

Mol Cell Proteomics. 2014 May;13(5):1392-6. doi: 10.1074/mcp.O113.037200. Epub 2014 Mar 3.


Matching cross-linked peptide spectra: only as good as the worse identification.

Trnka MJ, Baker PR, Robinson PJ, Burlingame AL, Chalkley RJ.

Mol Cell Proteomics. 2014 Feb;13(2):420-34. doi: 10.1074/mcp.M113.034009. Epub 2013 Dec 12.


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.

Skorobogatko Y, Landicho A, Chalkley RJ, Kossenkov AV, Gallo G, Vosseller K.

J Biol Chem. 2014 Feb 7;289(6):3602-12. doi: 10.1074/jbc.M113.512814. Epub 2013 Nov 26.


Proteome informatics research group (iPRG)_2012: a study on detecting modified peptides in a complex mixture.

Chalkley RJ, Bandeira N, Chambers MC, Clauser KR, Cottrell JS, Deutsch EW, Kapp EA, Lam HH, McDonald WH, Neubert TA, Sun RX.

Mol Cell Proteomics. 2014 Jan;13(1):360-71. doi: 10.1074/mcp.M113.032813. Epub 2013 Oct 31.


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.

Ni W, Xu SL, Chalkley RJ, Pham TN, Guan S, Maltby DA, Burlingame AL, Wang ZY, Quail PH.

Plant Cell. 2013 Jul;25(7):2679-98. doi: 10.1105/tpc.113.112342. Epub 2013 Jul 31.


Improving Peptide identification using empirical scoring systems.

Chalkley RJ.

Methods Mol Biol. 2013;1007:173-82. doi: 10.1007/978-1-62703-392-3_7.


Dissecting the roles of tyrosines 490 and 785 of TrkA protein in the induction of downstream protein phosphorylation using chimeric receptors.

Biarc J, Chalkley RJ, Burlingame AL, Bradshaw RA.

J Biol Chem. 2013 Jun 7;288(23):16606-18. doi: 10.1074/jbc.M113.475285. Epub 2013 Apr 15.


Glucose sensor O-GlcNAcylation coordinates with phosphorylation to regulate circadian clock.

Kaasik K, Kivimäe S, Allen JJ, Chalkley RJ, Huang Y, Baer K, Kissel H, Burlingame AL, Shokat KM, Ptáček LJ, Fu YH.

Cell Metab. 2013 Feb 5;17(2):291-302. doi: 10.1016/j.cmet.2012.12.017.


Rearrangements within human spliceosomes captured after exon ligation.

Ilagan JO, Chalkley RJ, Burlingame AL, Jurica MS.

RNA. 2013 Mar;19(3):400-12. doi: 10.1261/rna.034223.112. Epub 2013 Jan 23.


When target-decoy false discovery rate estimations are inaccurate and how to spot instances.

Chalkley RJ.

J Proteome Res. 2013 Feb 1;12(2):1062-4. doi: 10.1021/pr301063v. Epub 2013 Jan 18.


Receptor tyrosine kinase signaling mechanisms: Devolving TrkA responses with phosphoproteomics.

Bradshaw RA, Chalkley RJ, Biarc J, Burlingame AL.

Adv Biol Regul. 2013 Jan;53(1):87-96. doi: 10.1016/j.jbior.2012.10.006. Epub 2012 Nov 3. Review.


The DegraBase: a database of proteolysis in healthy and apoptotic human cells.

Crawford ED, Seaman JE, Agard N, Hsu GW, Julien O, Mahrus S, Nguyen H, Shimbo K, Yoshihara HA, Zhuang M, Chalkley RJ, Wells JA.

Mol Cell Proteomics. 2013 Mar;12(3):813-24. doi: 10.1074/mcp.O112.024372. Epub 2012 Dec 20.


Identification of O-linked β-D-N-acetylglucosamine-modified proteins from Arabidopsis.

Xu SL, Chalkley RJ, Wang ZY, Burlingame AL.

Methods Mol Biol. 2012;876:33-45. doi: 10.1007/978-1-61779-809-2_3.


Modification site localization scoring: strategies and performance.

Chalkley RJ, Clauser KR.

Mol Cell Proteomics. 2012 May;11(5):3-14. doi: 10.1074/mcp.R111.015305. Epub 2012 Feb 11. Review.


Rapid auxin-mediated changes in the proteome of the epidermal cells in rye coleoptiles: implications for the initiation of growth.

Deng Z, Xu S, Chalkley RJ, Oses-Prieto JA, Burlingame AL, Wang ZY, Kutschera U.

Plant Biol (Stuttg). 2012 May;14(3):420-7. doi: 10.1111/j.1438-8677.2011.00513.x. Epub 2011 Nov 25.


The induction of serine/threonine protein phosphorylations by a PDGFR/TrkA chimera in stably transfected PC12 cells.

Biarc J, Chalkley RJ, Burlingame AL, Bradshaw RA.

Mol Cell Proteomics. 2012 May;11(5):15-30. doi: 10.1074/mcp.M111.013375. Epub 2011 Oct 25.


The effect of using an inappropriate protein database for proteomic data analysis.

Knudsen GM, Chalkley RJ.

PLoS One. 2011;6(6):e20873. doi: 10.1371/journal.pone.0020873. Epub 2011 Jun 14.


Breaking up the C complex spliceosome shows stable association of proteins with the lariat intron intermediate.

Coltri P, Effenberger K, Chalkley RJ, Burlingame AL, Jurica MS.

PLoS One. 2011 Apr 19;6(4):e19061. doi: 10.1371/journal.pone.0019061.


Modification site localization scoring integrated into a search engine.

Baker PR, Trinidad JC, Chalkley RJ.

Mol Cell Proteomics. 2011 Jul;10(7):M111.008078. doi: 10.1074/mcp.M111.008078. Epub 2011 Apr 13.


Receptor tyrosine kinase signaling--a proteomic perspective.

Biarc J, Chalkley RJ, Burlingame AL, Bradshaw RA.

Adv Enzyme Regul. 2011;51(1):293-305. doi: 10.1016/j.advenzreg.2010.10.005. Epub 2010 Nov 5. Review.


Improved identification of O-linked glycopeptides from ETD data with optimized scoring for different charge states and cleavage specificities.

Darula Z, Chalkley RJ, Lynn A, Baker PR, Medzihradszky KF.

Amino Acids. 2011 Jul;41(2):321-8. doi: 10.1007/s00726-010-0692-2. Epub 2010 Jul 23.


Protein PTMs: post-translational modifications or pesky trouble makers?

Bradshaw RA, Medzihradszky KF, Chalkley RJ.

J Mass Spectrom. 2010 Oct;45(10):1095-7. doi: 10.1002/jms.1786.


Mass spectrometric analysis, automated identification and complete annotation of O-linked glycopeptides.

Darula Z, Chalkley RJ, Baker P, Burlingame AL, Medzihradszky KF.

Eur J Mass Spectrom (Chichester). 2010;16(3):421-8. doi: 10.1255/ejms.1028.


The transcriptional coactivator DRIP/mediator complex is involved in vitamin D receptor function and regulates keratinocyte proliferation and differentiation.

Oda Y, Chalkley RJ, Burlingame AL, Bikle DD.

J Invest Dermatol. 2010 Oct;130(10):2377-88. doi: 10.1038/jid.2010.148. Epub 2010 Jun 3.


Improving software performance for peptide electron transfer dissociation data analysis by implementation of charge state- and sequence-dependent scoring.

Baker PR, Medzihradszky KF, Chalkley RJ.

Mol Cell Proteomics. 2010 Sep;9(9):1795-803. doi: 10.1074/mcp.M110.000422. Epub 2010 May 31.


Phosphopeptide screen uncovers novel phosphorylation sites of Nedd4-2 that potentiate its inhibition of the epithelial Na+ channel.

Hallows KR, Bhalla V, Oyster NM, Wijngaarden MA, Lee JK, Li H, Chandran S, Xia X, Huang Z, Chalkley RJ, Burlingame AL, Pearce D.

J Biol Chem. 2010 Jul 9;285(28):21671-8. doi: 10.1074/jbc.M109.084731. Epub 2010 May 13.

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