Robert Chalkley, PhD

Title(s)Professional Researcher, Pharmaceutical Chemistry
SchoolSchool of Pharmacy
Address600 16th St, #N474A
San Francisco CA 94158
Phone415-476-5189
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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.
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    1. Assessing Heterogeneity in the N-Telopeptides of Type I Collagen by Mass Spectrometry. bioRxiv. 2024 Mar 31. 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. PMID: 38585857; PMCID: PMC10996605.
      View in: PubMed   Mentions:
    2. A Legionella toxin exhibits tRNA mimicry and glycosyl transferase activity to target the translation machinery and trigger a ribotoxic stress response. Nat Cell Biol. 2023 Nov; 25(11):1600-1615. 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. PMID: 37857833.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansCells
    3. SPINDLY mediates O-fucosylation of hundreds of proteins and sugar-dependent growth in Arabidopsis. Plant Cell. 2023 04 20; 35(5):1318-1333. 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. PMID: 36739885; PMCID: PMC10118272.
      View in: PubMed   Mentions: 6     Fields:    Translation:Animals
    4. Chemical Genetic Identification of PKC Epsilon Substrates in Mouse Brain. Mol Cell Proteomics. 2023 04; 22(4):100522. Dugan MP, Ferguson LB, Hertz NT, Chalkley RJ, Burlingame AL, Shokat KM, Parker PJ, Messing RO. PMID: 36863607; PMCID: PMC10105488.
      View in: PubMed   Mentions: 1     Fields:    Translation:AnimalsCells
    5. Capture, Release, and Identification of Newly Synthesized Proteins for Improved Profiling of Functional Translatomes. Mol Cell Proteomics. 2023 03; 22(3):100497. Phillips NJ, Vinaithirthan BM, Oses-Prieto JA, Chalkley RJ, Burlingame AL. PMID: 36642223; PMCID: PMC9971285.
      View in: PubMed   Mentions:    Fields:    
    6. Application of Parallel Reaction Monitoring in 15N Labeled Samples for Quantification. Front Plant Sci. 2022; 13:832585. Reyes AV, Shrestha R, Baker PR, Chalkley RJ, Xu SL. PMID: 35592564; PMCID: PMC9111532.
      View in: PubMed   Mentions: 1  
    7. 15N Metabolic Labeling Quantification Workflow in Arabidopsis Using Protein Prospector. Front Plant Sci. 2022; 13:832562. Shrestha R, Reyes AV, Baker PR, Wang ZY, Chalkley RJ, Xu SL. PMID: 35242158; PMCID: PMC8885517.
      View in: PubMed   Mentions: 6  
    8. Modulating environmental signals to reveal mechanisms and vulnerabilities of cancer persisters. Sci Adv. 2022 01 28; 8(4):eabi7711. Sun X, Bieber JM, Hammerlindl H, Chalkley RJ, Li KH, Burlingame AL, Jacobson MP, Wu LF, Altschuler SJ. PMID: 35089788; PMCID: PMC8797778.
      View in: PubMed   Mentions: 1     Fields:    Translation:Humans
    9. Author Correction: Community evaluation of glycoproteomics informatics solutions reveals high-performance search strategies for serum glycopeptide analysis. Nat Methods. 2022 Jan; 19(1):130. 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, Nguyen-Khuong T, Nilsson J, Pap A, Park GW, Parker BL, Pegg CL, Penninger JM, Phung TK, Pioch M, Rapp E, Sakalli E, Sanda M, Schulz BL, Scott NE, Sofronov G, Stadlmann J, Vakhrushev SY, Woo CM, Wu HY, Yang P, Ying W, Zhang H, Zhang Y, Zhao J, Zaia J, Haslam SM, Palmisano G, Yoo JS, Larson G, Khoo KH, Medzihradszky KF, Kolarich D, Packer NH, Thaysen-Andersen M. PMID: 34893784; PMCID: PMC8748192.
      View in: PubMed   Mentions:    Fields:    
    10. Community evaluation of glycoproteomics informatics solutions reveals high-performance search strategies for serum glycopeptide analysis. Nat Methods. 2021 11; 18(11):1304-1316. 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, Nguyen-Khuong T, Nilsson J, Pap A, Park GW, Parker BL, Pegg CL, Penninger JM, Phung TK, Pioch M, Rapp E, Sakalli E, Sanda M, Schulz BL, Scott NE, Sofronov G, Stadlmann J, Vakhrushev SY, Woo CM, Wu HY, Yang P, Ying W, Zhang H, Zhang Y, Zhao J, Zaia J, Haslam SM, Palmisano G, Yoo JS, Larson G, Khoo KH, Medzihradszky KF, Kolarich D, Packer NH, Thaysen-Andersen M. PMID: 34725484; PMCID: PMC8566223.
      View in: PubMed   Mentions: 36     Fields:    Translation:HumansCells
    11. Methods for Enrichment and Assignment of N-Acetylglucosamine Modification Sites. Mol Cell Proteomics. 2021; 20:100031. Maynard JC, Chalkley RJ. PMID: 32938750; PMCID: PMC8724609.
      View in: PubMed   Mentions: 9     Fields:    
    12. Proteomic analysis of platelet-rich and platelet-poor plasma. Regen Ther. 2020 Dec; 15:226-235. Miroshnychenko O, Chalkley RJ, Leib RD, Everts PA, Dragoo JL. PMID: 33426223; PMCID: PMC7770407.
      View in: PubMed   Mentions: 9  
    13. Toward Increased Reliability, Transparency, and Accessibility in Cross-linking Mass Spectrometry. Structure. 2020 11 03; 28(11):1259-1268. 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, Mechtler K, Moritz RL, Netz E, Novak P, Petrotchenko E, Sali A, Scheltema RA, Schmidt C, Schriemer D, Sinz A, Sobott F, Stengel F, Thalassinos K, Urlaub H, Viner R, Vizcaíno JA, Wilkins MR, Rappsilber J. PMID: 33065067.
      View in: PubMed   Mentions: 14     Fields:    Translation:HumansCells
    14. Characterization of Prenylated C-terminal Peptides Using a Thiopropyl-based Capture Technique and LC-MS/MS. Mol Cell Proteomics. 2020 06; 19(6):1005-1016. Wilkins JA, Kaasik K, Chalkley RJ, Burlingame AL. PMID: 32284353; PMCID: PMC7261820.
      View in: PubMed   Mentions: 3     Fields:    Translation:AnimalsCells
    15. The effectiveness of filtering glycopeptide peak list files for Y ions. Mol Omics. 2020 04 01; 16(2):147-155. Chalkley RJ, Medzihradszky KF, Darula Z, Pap A, Baker PR. PMID: 32065175.
      View in: PubMed   Mentions: 7     Fields:    Translation:Humans
    16. A two-step probing method to compare lysine accessibility across macromolecular complex conformations. RNA Biol. 2019 10; 16(10):1346-1354. MacRae AJ, Coltri P, Hrabeta-Robinson E, Chalkley RJ, Burlingame AL, Jurica MS. PMID: 31213125; PMCID: PMC6779377.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    17. Proteomics Standards Initiative Extended FASTA Format. J Proteome Res. 2019 06 07; 18(6):2686-2692. 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 PR, Collins A, Van Den Bossche T, Deutsch EW. PMID: 31081335; PMCID: PMC6642660.
      View in: PubMed   Mentions: 14     Fields:    Translation:Humans
    18. Initial Guidelines for Manuscripts Employing Data-independent Acquisition Mass Spectrometry for Proteomic Analysis. Mol Cell Proteomics. 2019 01; 18(1):1-2. Chalkley RJ, MacCoss MJ, Jaffe JD, Röst HL. PMID: 30602589; PMCID: PMC6317474.
      View in: PubMed   Mentions: 5     Fields:    Translation:Humans
    19. Expanding the Use of Spectral Libraries in Proteomics. J Proteome Res. 2018 12 07; 17(12):4051-4060. 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. PMID: 30270626; PMCID: PMC6443480.
      View in: PubMed   Mentions: 20     Fields:    Translation:HumansAnimalsCells
    20. Prp8 positioning of U5 snRNA is linked to 5' splice site recognition. RNA. 2018 06; 24(6):769-777. MacRae AJ, Mayerle M, Hrabeta-Robinson E, Chalkley RJ, Guthrie C, Burlingame AL, Jurica MS. PMID: 29487104; PMCID: PMC5959246.
      View in: PubMed   Mentions: 9     Fields:    Translation:HumansAnimalsCells
    21. Revealing nascent proteomics in signaling pathways and cell differentiation. Proc Natl Acad Sci U S A. 2018 03 06; 115(10):2353-2358. Forester CM, Zhao Q, Phillips NJ, Urisman A, Chalkley RJ, Oses-Prieto JA, Zhang L, Ruggero D, Burlingame AL. PMID: 29467287; PMCID: PMC5877968.
      View in: PubMed   Mentions: 24     Fields:    Translation:HumansCells
    22. Peripheral Elevation of a Klotho Fragment Enhances Brain Function and Resilience in Young, Aging, and α-Synuclein Transgenic Mice. Cell Rep. 2017 08 08; 20(6):1360-1371. Leon J, Moreno AJ, Garay BI, Chalkley RJ, Burlingame AL, Wang D, Dubal DB. PMID: 28793260; PMCID: PMC5816951.
      View in: PubMed   Mentions: 52     Fields:    Translation:AnimalsCells
    23. The mzIdentML Data Standard Version 1.2, Supporting Advances in Proteome Informatics. Mol Cell Proteomics. 2017 07; 16(7):1275-1285. 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. PMID: 28515314; PMCID: PMC5500760.
      View in: PubMed   Mentions: 28     Fields:    
    24. PPKs mediate direct signal transfer from phytochrome photoreceptors to transcription factor PIF3. Nat Commun. 2017 05 11; 8:15236. Ni W, Xu SL, González-Grandío E, Chalkley RJ, Huhmer AFR, Burlingame AL, Wang ZY, Quail PH. PMID: 28492231; PMCID: PMC5437280.
      View in: PubMed   Mentions: 75     Fields:    Translation:AnimalsCells
    25. Hyper-O-GlcNAcylation activates nuclear factor κ-light-chain-enhancer of activated B cells (NF-κB) signaling through interplay with phosphorylation and acetylation. J Biol Chem. 2017 06 02; 292(22):9150-9163. Ma Z, Chalkley RJ, Vosseller K. PMID: 28416608; PMCID: PMC5454098.
      View in: PubMed   Mentions: 32     Fields:    Translation:HumansAnimalsCells
    26. New Guidelines for Publication of Manuscripts Describing Development and Application of Targeted Mass Spectrometry Measurements of Peptides and Proteins. Mol Cell Proteomics. 2017 03; 16(3):327-328. 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, Vitek O, Zimmerman L. PMID: 28183812; PMCID: PMC5340997.
      View in: PubMed   Mentions: 17     Fields:    
    27. Proteomic analysis reveals O-GlcNAc modification on proteins with key regulatory functions in Arabidopsis. Proc Natl Acad Sci U S A. 2017 02 21; 114(8):E1536-E1543. Xu SL, Chalkley RJ, Maynard JC, Wang W, Ni W, Jiang X, Shin K, Cheng L, Savage D, Hühmer AF, Burlingame AL, Wang ZY. PMID: 28154133; PMCID: PMC5338445.
      View in: PubMed   Mentions: 49     Fields:    Translation:AnimalsCells
    28. Use of a glycosylation site database to improve glycopeptide identification from complex mixtures. Anal Bioanal Chem. 2017 Jan; 409(2):571-577. Chalkley RJ, Baker PR. PMID: 27722944.
      View in: PubMed   Mentions: 10     Fields:    Translation:Cells
    29. N-Glycopeptide Profiling in Arabidopsis Inflorescence. Mol Cell Proteomics. 2016 06; 15(6):2048-54. Xu SL, Medzihradszky KF, Wang ZY, Burlingame AL, Chalkley RJ. PMID: 27067053; PMCID: PMC5083099.
      View in: PubMed   Mentions: 13     Fields:    Translation:AnimalsCells
    30. Glyco-centric lectin magnetic bead array (LeMBA) - proteomics dataset of human serum samples from healthy, Barrett׳s esophagus and esophageal adenocarcinoma individuals. Data Brief. 2016 Jun; 7:1058-62. 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. PMID: 27408916; PMCID: PMC4927955.
      View in: PubMed   Mentions: 1  
    31. Modification Site Localization in Peptides. Adv Exp Med Biol. 2016; 919:243-247. Chalkley RJ. PMID: 27975222.
      View in: PubMed   Mentions:    Fields:    Translation:HumansAnimalsCells
    32. Use of a mutant OGA for detecting O-GlcNAc modified proteins. Biochem J. 2015 Dec 01; 472(2):e25-6. Chalkley RJ. PMID: 26567273.
      View in: PubMed   Mentions:    Fields:    Translation:HumansAnimals
    33. On Credibility, Clarity, and Compliance. Mol Cell Proteomics. 2015 Jul; 14(7):1731-3. Burlingame A, Carr SA, Bradshaw RA, Bradshaw RA, Chalkley RJ. PMID: 26041845; PMCID: PMC4587320.
      View in: PubMed   Mentions: 8     Fields:    
    34. Proteotranscriptomic Profiling of 231-BR Breast Cancer Cells: Identification of Potential Biomarkers and Therapeutic Targets for Brain Metastasis. Mol Cell Proteomics. 2015 Sep; 14(9):2316-30. Dun MD, Chalkley RJ, Faulkner S, Keene S, Avery-Kiejda KA, Scott RJ, Falkenby LG, Cairns MJ, Larsen MR, Bradshaw RA, Hondermarck H. PMID: 26041846; PMCID: PMC4563718.
      View in: PubMed   Mentions: 31     Fields:    Translation:HumansCells
    35. Tissue-Specific Glycosylation at the Glycopeptide Level. Mol Cell Proteomics. 2015 Aug; 14(8):2103-10. Medzihradszky KF, Kaasik K, Chalkley RJ. PMID: 25995273; PMCID: PMC4528240.
      View in: PubMed   Mentions: 56     Fields:    Translation:AnimalsCells
    36. Characterizing sialic acid variants at the glycopeptide level. Anal Chem. 2015 Mar 03; 87(5):3064-71. Medzihradszky KF, Kaasik K, Chalkley RJ. PMID: 25654559; PMCID: PMC4367445.
      View in: PubMed   Mentions: 22     Fields:    Translation:AnimalsCells
    37. Lessons in de novo peptide sequencing by tandem mass spectrometry. Mass Spectrom Rev. 2015 Jan-Feb; 34(1):43-63. Medzihradszky KF, Chalkley RJ. PMID: 25667941; PMCID: PMC4367481.
      View in: PubMed   Mentions: 60     Fields:    Translation:Cells
    38. NGF and ProNGF: Regulation of neuronal and neoplastic responses through receptor signaling. Adv Biol Regul. 2015 May; 58:16-27. Bradshaw RA, Bradshaw RA, Pundavela J, Biarc J, Chalkley RJ, Burlingame AL, Hondermarck H. PMID: 25491371; PMCID: PMC4426037.
      View in: PubMed   Mentions: 48     Fields:    Translation:HumansAnimalsCells
    39. A standardized framing for reporting protein identifications in mzIdentML 1.2. Proteomics. 2014 Nov; 14(21-22):2389-99. 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. PMID: 25092112; PMCID: PMC4384534.
      View in: PubMed   Mentions: 9     Fields:    Translation:Humans
    40. Molecular architecture of photoreceptor phosphodiesterase elucidated by chemical cross-linking and integrative modeling. J Mol Biol. 2014 Nov 11; 426(22):3713-3728. Zeng-Elmore X, Gao XZ, Pellarin R, Schneidman-Duhovny D, Zhang XJ, Kozacka KA, Tang Y, Sali A, Chalkley RJ, Cote RH, Chu F. PMID: 25149264; PMCID: PMC4253074.
      View in: PubMed   Mentions: 29     Fields:    Translation:AnimalsCells
    41. Double impact of cigarette smoke and mechanical ventilation on the alveolar epithelial type II cell. Crit Care. 2014 Mar 25; 18(2):R50. Hirsch J, Chalkley RJ, Bentley T, Burlingame AL, Frank JA. PMID: 24666941; PMCID: PMC4056080.
      View in: PubMed   Mentions: 11     Fields:    Translation:AnimalsPHPublic Health
    42. MS-viewer: a web-based spectral viewer for proteomics results. Mol Cell Proteomics. 2014 May; 13(5):1392-6. Baker PR, Chalkley RJ. PMID: 24591702; PMCID: PMC4014294.
      View in: PubMed   Mentions: 91     Fields:    
    43. ProteomeXchange provides globally coordinated proteomics data submission and dissemination. Nat Biotechnol. 2014 Mar; 32(3):223-6. 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. PMID: 24727771; PMCID: PMC3986813.
      View in: PubMed   Mentions: 1375     Fields:    Translation:HumansAnimals
    44. Matching cross-linked peptide spectra: only as good as the worse identification. Mol Cell Proteomics. 2014 Feb; 13(2):420-34. Trnka MJ, Baker PR, Robinson PJ, Burlingame AL, Chalkley RJ. PMID: 24335475; PMCID: PMC3916644.
      View in: PubMed   Mentions: 91     Fields:    Translation:HumansCells
    45. 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. J Biol Chem. 2014 Feb 07; 289(6):3602-12. Skorobogatko Y, Landicho A, Chalkley RJ, Kossenkov AV, Gallo G, Vosseller K. PMID: 24280219; PMCID: PMC3916560.
      View in: PubMed   Mentions: 23     Fields:    Translation:HumansAnimalsCells
    46. Proteome informatics research group (iPRG)_2012: a study on detecting modified peptides in a complex mixture. Mol Cell Proteomics. 2014 Jan; 13(1):360-71. Chalkley RJ, Bandeira N, Chambers MC, Clauser KR, Cottrell JS, Deutsch EW, Kapp EA, Lam HH, McDonald WH, Neubert TA, Sun RX. PMID: 24187338; PMCID: PMC3879627.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansCells
    47. 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. Plant Cell. 2013 Jul; 25(7):2679-98. Ni W, Xu SL, Chalkley RJ, Pham TN, Guan S, Maltby DA, Burlingame AL, Wang ZY, Quail PH. PMID: 23903316; PMCID: PMC3753391.
      View in: PubMed   Mentions: 74     Fields:    Translation:AnimalsCells
    48. Dissecting the roles of tyrosines 490 and 785 of TrkA protein in the induction of downstream protein phosphorylation using chimeric receptors. J Biol Chem. 2013 Jun 07; 288(23):16606-16618. Biarc J, Chalkley RJ, Burlingame AL, Bradshaw RA, Bradshaw RA. PMID: 23589303; PMCID: PMC3675596.
      View in: PubMed   Mentions: 9     Fields:    Translation:HumansAnimalsCells
    49. Glucose sensor O-GlcNAcylation coordinates with phosphorylation to regulate circadian clock. Cell Metab. 2013 Feb 05; 17(2):291-302. Kaasik K, Kivimäe S, Allen JJ, Chalkley RJ, Huang Y, Baer K, Kissel H, Burlingame AL, Shokat KM, Ptácek LJ, Fu YH. PMID: 23395175; PMCID: PMC3597447.
      View in: PubMed   Mentions: 129     Fields:    Translation:HumansAnimalsCells
    50. Rearrangements within human spliceosomes captured after exon ligation. RNA. 2013 Mar; 19(3):400-12. Ilagan JO, Chalkley RJ, Burlingame AL, Jurica MS. PMID: 23345524; PMCID: PMC3677250.
      View in: PubMed   Mentions: 24     Fields:    Translation:HumansAnimalsCells
    51. When target-decoy false discovery rate estimations are inaccurate and how to spot instances. J Proteome Res. 2013 Feb 01; 12(2):1062-4. Chalkley RJ. PMID: 23298186; PMCID: PMC4751987.
      View in: PubMed   Mentions: 8     Fields:    
    52. Improving Peptide identification using empirical scoring systems. Methods Mol Biol. 2013; 1007:173-82. Chalkley RJ. PMID: 23666726; PMCID: PMC4313727.
      View in: PubMed   Mentions: 4     Fields:    Translation:Cells
    53. The DegraBase: a database of proteolysis in healthy and apoptotic human cells. Mol Cell Proteomics. 2013 Mar; 12(3):813-24. Crawford ED, Seaman JE, Agard N, Hsu GW, Julien O, Mahrus S, Nguyen H, Shimbo K, Yoshihara HA, Zhuang M, Chalkley RJ, Wells JA. PMID: 23264352; PMCID: PMC3591672.
      View in: PubMed   Mentions: 67     Fields:    Translation:HumansCells
    54. Modification site localization scoring: strategies and performance. Mol Cell Proteomics. 2012 May; 11(5):3-14. Chalkley RJ, Clauser KR. PMID: 22328712; PMCID: PMC3418845.
      View in: PubMed   Mentions: 46     Fields:    Translation:HumansCells
    55. Identification of O-linked β-D-N-acetylglucosamine-modified proteins from Arabidopsis. Methods Mol Biol. 2012; 876:33-45. Xu SL, Chalkley RJ, Wang ZY, Burlingame AL. PMID: 22576084; PMCID: PMC3699408.
      View in: PubMed   Mentions: 7     Fields:    
    56. The induction of serine/threonine protein phosphorylations by a PDGFR/TrkA chimera in stably transfected PC12 cells. Mol Cell Proteomics. 2012 May; 11(5):15-30. Biarc J, Chalkley RJ, Burlingame AL, Bradshaw RA, Bradshaw RA. PMID: 22027198; PMCID: PMC3418849.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansAnimalsCells
    57. The effect of using an inappropriate protein database for proteomic data analysis. PLoS One. 2011; 6(6):e20873. Knudsen GM, Chalkley RJ. PMID: 21695130; PMCID: PMC3114852.
      View in: PubMed   Mentions: 25     Fields:    Translation:AnimalsCells
    58. Breaking up the C complex spliceosome shows stable association of proteins with the lariat intron intermediate. PLoS One. 2011 Apr 19; 6(4):e19061. Coltri P, Effenberger K, Chalkley RJ, Burlingame AL, Jurica MS. PMID: 21526149; PMCID: PMC3079748.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansCells
    59. Modification site localization scoring integrated into a search engine. Mol Cell Proteomics. 2011 Jul; 10(7):M111.008078. Baker PR, Trinidad JC, Chalkley RJ. PMID: 21490164; PMCID: PMC3134073.
      View in: PubMed   Mentions: 58     Fields:    Translation:Cells
    60. Receptor tyrosine kinase signaling--a proteomic perspective. Adv Enzyme Regul. 2011; 51(1):293-305. Biarc J, Chalkley RJ, Burlingame AL, Bradshaw RA, Bradshaw RA. PMID: 21056590; PMCID: PMC3079071.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansAnimalsCells
    61. Protein PTMs: post-translational modifications or pesky trouble makers? J Mass Spectrom. 2010 Oct; 45(10):1095-7. Bradshaw RA, Medzihradszky KF, Chalkley RJ. PMID: 20635432; PMCID: PMC3133960.
      View in: PubMed   Mentions: 8     Fields:    Translation:Cells
    62. Improved identification of O-linked glycopeptides from ETD data with optimized scoring for different charge states and cleavage specificities. Amino Acids. 2011 Jul; 41(2):321-8. Darula Z, Chalkley RJ, Lynn A, Baker PR, Medzihradszky KF. PMID: 20652609; PMCID: PMC3102200.
      View in: PubMed   Mentions: 14     Fields:    Translation:AnimalsCells
    63. The transcriptional coactivator DRIP/mediator complex is involved in vitamin D receptor function and regulates keratinocyte proliferation and differentiation. J Invest Dermatol. 2010 Oct; 130(10):2377-88. Oda Y, Chalkley RJ, Burlingame AL, Bikle DD. PMID: 20520624; PMCID: PMC4114506.
      View in: PubMed   Mentions: 20     Fields:    Translation:HumansCells
    64. Improving software performance for peptide electron transfer dissociation data analysis by implementation of charge state- and sequence-dependent scoring. Mol Cell Proteomics. 2010 Sep; 9(9):1795-803. Baker PR, Medzihradszky KF, Chalkley RJ. PMID: 20513802; PMCID: PMC2938109.
      View in: PubMed   Mentions: 35     Fields:    Translation:Cells
    65. Phosphopeptide screen uncovers novel phosphorylation sites of Nedd4-2 that potentiate its inhibition of the epithelial Na+ channel. J Biol Chem. 2010 Jul 09; 285(28):21671-8. Hallows KR, Bhalla V, Oyster NM, Wijngaarden MA, Lee JK, Li H, Chandran S, Xia X, Huang Z, Chalkley RJ, Burlingame AL, Pearce D. PMID: 20466724; PMCID: PMC2898378.
      View in: PubMed   Mentions: 25     Fields:    Translation:HumansAnimalsCells
    66. The RasGAP proteins Ira2 and neurofibromin are negatively regulated by Gpb1 in yeast and ETEA in humans. Mol Cell Biol. 2010 May; 30(9):2264-79. Phan VT, Ding VW, Li F, Chalkley RJ, Burlingame A, McCormick F. PMID: 20160012; PMCID: PMC2863595.
      View in: PubMed   Mentions: 34     Fields:    Translation:HumansAnimalsCells
    67. Statistical analysis of Peptide electron transfer dissociation fragmentation mass spectrometry. Anal Chem. 2010 Jan 15; 82(2):579-84. Chalkley RJ, Medzihradszky KF, Lynn AJ, Baker PR, Burlingame AL. PMID: 20028093; PMCID: PMC2836188.
      View in: PubMed   Mentions: 25     Fields:    Translation:Cells
    68. Mass spectrometric analysis, automated identification and complete annotation of O-linked glycopeptides. Eur J Mass Spectrom (Chichester). 2010; 16(3):421-8. Darula Z, Chalkley RJ, Baker P, Burlingame AL, Medzihradszky KF. PMID: 20530845; PMCID: PMC2963623.
      View in: PubMed   Mentions: 19     Fields:    Translation:Cells
    69. Instrumentation for LC-MS/MS in proteomics. Methods Mol Biol. 2010; 658:47-60. Chalkley R. PMID: 20839097.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansAnimals
    70. Finding chimeras: a bioinformatics strategy for identification of cross-linked peptides. Mol Cell Proteomics. 2010 Jan; 9(1):25-31. Chu F, Baker PR, Burlingame AL, Chalkley RJ. PMID: 19809093; PMCID: PMC2808265.
      View in: PubMed   Mentions: 44     Fields:    Translation:Cells
    71. The role of exon sequences in C complex spliceosome structure. J Mol Biol. 2009 Nov 27; 394(2):363-75. Ilagan J, Yuh P, Chalkley RJ, Burlingame AL, Jurica MS. PMID: 19761775; PMCID: PMC2783800.
      View in: PubMed   Mentions: 13     Fields:    Translation:Cells
    72. Recommendations from the 2008 International Summit on Proteomics Data Release and Sharing Policy: the Amsterdam principles. J Proteome Res. 2009 Jul; 8(7):3689-92. 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, Nesvizhskii A, Ping P, Pontén F, Yang L, Yates JR, Stein SE, Hermjakob H, Kinsinger CR, Apweiler R. PMID: 19344107; PMCID: PMC2742685.
      View in: PubMed   Mentions: 29     Fields:    Translation:Humans
    73. Identification of protein O-GlcNAcylation sites using electron transfer dissociation mass spectrometry on native peptides. Proc Natl Acad Sci U S A. 2009 Jun 02; 106(22):8894-9. Chalkley RJ, Thalhammer A, Schoepfer R, Burlingame AL. PMID: 19458039; PMCID: PMC2690010.
      View in: PubMed   Mentions: 125     Fields:    Translation:AnimalsCells
    74. HDL antielastase activity prevents smooth muscle cell anoikis, a potential new antiatherogenic property. FASEB J. 2009 Sep; 23(9):3129-39. 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. PMID: 19417089; PMCID: PMC2735359.
      View in: PubMed   Mentions: 46     Fields:    Translation:HumansCells
    75. 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. J Mol Med (Berl). 2009 May; 87(5):507-14. Conrad F, Zhu X, Zhang X, Chalkley RJ, Burlingame AL, Marks JD, Liu B. PMID: 19219419; PMCID: PMC2796542.
      View in: PubMed   Mentions: 14     Fields:    Translation:HumansAnimalsCells
    76. Identification of new p53 acetylation sites in COS-1 cells. Mol Cell Proteomics. 2009 Jun; 8(6):1167-73. Joubel A, Chalkley RJ, Medzihradszky KF, Hondermarck H, Burlingame AL. PMID: 19155208; PMCID: PMC2690490.
      View in: PubMed   Mentions: 5     Fields:    Translation:AnimalsCells
    77. The PSI-MOD community standard for representation of protein modification data. Nat Biotechnol. 2008 Aug; 26(8):864-6. Montecchi-Palazzi L, Beavis R, Binz PA, Chalkley RJ, Cottrell J, Creasy D, Shofstahl J, Seymour SL, Garavelli JS. PMID: 18688235.
      View in: PubMed   Mentions: 89     Fields:    Translation:Cells
    78. In-depth analysis of tandem mass spectrometry data from disparate instrument types. Mol Cell Proteomics. 2008 Dec; 7(12):2386-98. Chalkley RJ, Baker PR, Medzihradszky KF, Lynn AJ, Burlingame AL. PMID: 18653769; PMCID: PMC2596346.
      View in: PubMed   Mentions: 105     Fields:    Translation:Cells
    79. Cell cycle-dependent phosphorylation of human CDC5 regulates RNA processing. Cell Cycle. 2008 Jun 15; 7(12):1795-803. Gräub R, Lancero H, Pedersen A, Chu M, Padmanabhan K, Xu XQ, Spitz P, Chalkley R, Burlingame AL, Stokoe D, Bernstein HS. PMID: 18583928; PMCID: PMC2940709.
      View in: PubMed   Mentions: 13     Fields:    Translation:HumansAnimalsCells
    80. A proteomics study of brassinosteroid response in Arabidopsis. Mol Cell Proteomics. 2007 Dec; 6(12):2058-71. 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. PMID: 17848588; PMCID: PMC2966871.
      View in: PubMed   Mentions: 53     Fields:    Translation:AnimalsCells
    81. Impact of low and high tidal volumes on the rat alveolar epithelial type II cell proteome. Am J Respir Crit Care Med. 2007 May 15; 175(10):1006-13. Hirsch J, Hansen KC, Sapru A, Frank JA, Chalkley RJ, Fang X, Trinidad JC, Baker P, Burlingame AL, Matthay MA. PMID: 17363773; PMCID: PMC1899270.
      View in: PubMed   Mentions: 10     Fields:    Translation:AnimalsCells
    82. Side-chain fragmentation of alkylated cysteine residues in electron capture dissociation mass spectrometry. J Am Soc Mass Spectrom. 2006 Sep; 17(9):1271-4. Chalkley RJ, Brinkworth CS, Burlingame AL. PMID: 16809046.
      View in: PubMed   Mentions: 17     Fields:    Translation:Cells
    83. Keratin 20 serine 13 phosphorylation is a stress and intestinal goblet cell marker. J Biol Chem. 2006 Jun 16; 281(24):16453-61. Zhou Q, Cadrin M, Herrmann H, Chen CH, Chalkley RJ, Burlingame AL, Omary MB. PMID: 16608857.
      View in: PubMed   Mentions: 21     Fields:    Translation:HumansAnimalsCells
    84. O-linked N-acetylglucosamine proteomics of postsynaptic density preparations using lectin weak affinity chromatography and mass spectrometry. Mol Cell Proteomics. 2006 May; 5(5):923-34. Vosseller K, Trinidad JC, Chalkley RJ, Specht CG, Thalhammer A, Lynn AJ, Snedecor JO, Guan S, Medzihradszky KF, Maltby DA, Schoepfer R, Burlingame AL. PMID: 16452088.
      View in: PubMed   Mentions: 166     Fields:    Translation:AnimalsCells
    85. Mapping post-translational modifications of the histone variant MacroH2A1 using tandem mass spectrometry. Mol Cell Proteomics. 2006 Jan; 5(1):194-203. Chu F, Nusinow DA, Chalkley RJ, Plath K, Panning B, Burlingame AL. PMID: 16210244.
      View in: PubMed   Mentions: 36     Fields:    Translation:Cells
    86. Mass spectrometric analysis of histone posttranslational modifications. Methods. 2005 Aug; 36(4):383-94. Burlingame AL, Zhang X, Chalkley RJ. PMID: 16112065.
      View in: PubMed   Mentions: 11     Fields:    Translation:HumansAnimalsCells
    87. A combinatorial code for the interaction of alpha-synuclein with membranes. J Biol Chem. 2005 Sep 09; 280(36):31664-72. Kubo S, Nemani VM, Chalkley RJ, Anthony MD, Hattori N, Mizuno Y, Edwards RH, Fortin DL. PMID: 16020543.
      View in: PubMed   Mentions: 86     Fields:    Translation:HumansAnimalsCells
    88. 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. Mol Cell Proteomics. 2005 Aug; 4(8):1194-204. Chalkley RJ, Baker PR, Huang L, Hansen KC, Allen NP, Rexach M, Burlingame AL. PMID: 15937296.
      View in: PubMed   Mentions: 81     Fields:    Translation:Humans
    89. 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? Mol Cell Proteomics. 2005 Aug; 4(8):1189-93. Chalkley RJ, Baker PR, Hansen KC, Medzihradszky KF, Allen NP, Rexach M, Burlingame AL. PMID: 15923566.
      View in: PubMed   Mentions: 22     Fields:    Translation:Humans
    90. Quantitative analysis of both protein expression and serine / threonine post-translational modifications through stable isotope labeling with dithiothreitol. Proteomics. 2005 Feb; 5(2):388-98. Vosseller K, Hansen KC, Chalkley RJ, Trinidad JC, Wells L, Hart GW, Burlingame AL. PMID: 15648052.
      View in: PubMed   Mentions: 51     Fields:    Translation:AnimalsCells
    91. Bioinformatic methods to exploit mass spectrometric data for proteomic applications. Methods Enzymol. 2005; 402:289-312. Chalkley RJ, Hansen KC, Baldwin MA. PMID: 16401513.
      View in: PubMed   Mentions: 18     Fields:    Translation:HumansAnimals
    92. The urinary proteome in Fanconi syndrome implies specificity in the reabsorption of proteins by renal proximal tubule cells. Am J Physiol Renal Physiol. 2004 Sep; 287(3):F353-64. Cutillas PR, Chalkley RJ, Hansen KC, Cramer R, Norden AG, Waterfield MD, Burlingame AL, Unwin RJ. PMID: 15140760.
      View in: PubMed   Mentions: 19     Fields:    Translation:Humans
    93. Two distinct coactivators, DRIP/mediator and SRC/p160, are differentially involved in VDR transactivation during keratinocyte differentiation. J Steroid Biochem Mol Biol. 2004 May; 89-90(1-5):273-6. Oda Y, Sihlbom C, Chalkley RJ, Huang L, Rachez C, Chang CP, Burlingame AL, Freedman LP, Bikle DD. PMID: 15225784.
      View in: PubMed   Mentions: 4     Fields:    Translation:AnimalsCells
    94. Regulated expression of apolipoprotein E by human retinal pigment epithelial cells. J Lipid Res. 2004 Feb; 45(2):263-71. Ishida BY, Bailey KR, Duncan KG, Chalkley RJ, Burlingame AL, Kane JP, Schwartz DM. PMID: 14594998.
      View in: PubMed   Mentions: 42     Fields:    Translation:HumansCells
    95. Two distinct coactivators, DRIP/mediator and SRC/p160, are differentially involved in vitamin D receptor transactivation during keratinocyte differentiation. Mol Endocrinol. 2003 Nov; 17(11):2329-39. Oda Y, Sihlbom C, Chalkley RJ, Huang L, Rachez C, Chang CP, Burlingame AL, Freedman LP, Bikle DD. PMID: 12893881.
      View in: PubMed   Mentions: 26     Fields:    Translation:HumansCells
    96. Mass spectrometric analysis of protein mixtures at low levels using cleavable 13C-isotope-coded affinity tag and multidimensional chromatography. Mol Cell Proteomics. 2003 May; 2(5):299-314. Hansen KC, Schmitt-Ulms G, Chalkley RJ, Hirsch J, Baldwin MA, Burlingame AL. PMID: 12766231.
      View in: PubMed   Mentions: 59     Fields:    Translation:HumansAnimalsCells
    97. Linking the T cell surface protein CD2 to the actin-capping protein CAPZ via CMS and CIN85. J Biol Chem. 2003 Jun 20; 278(25):22396-403. Hutchings NJ, Clarkson N, Chalkley R, Barclay AN, Brown MH. PMID: 12690097.
      View in: PubMed   Mentions: 41     Fields:    Translation:HumansCells
    98. Identification of novel sites of O-N-acetylglucosamine modification of serum response factor using quadrupole time-of-flight mass spectrometry. Mol Cell Proteomics. 2003 Mar; 2(3):182-90. Chalkley RJ, Burlingame AL. PMID: 12684542.
      View in: PubMed   Mentions: 16     Fields:    Translation:HumansCells
    99. Deciphering networks of protein interactions at the nuclear pore complex. Mol Cell Proteomics. 2002 Dec; 1(12):930-46. Allen NP, Patel SS, Huang L, Chalkley RJ, Burlingame A, Lutzmann M, Hurt EC, Rexach M. PMID: 12543930.
      View in: PubMed   Mentions: 37     Fields:    Translation:AnimalsCells
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