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For: Ferries S, Perkins S, Brownridge PJ, Campbell A, Eyers PA, Jones AR, Eyers CE. Evaluation of Parameters for Confident Phosphorylation Site Localization Using an Orbitrap Fusion Tribrid Mass Spectrometer. J Proteome Res 2017;16:3448-3459. [DOI: 10.1021/acs.jproteome.7b00337] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Number Cited by Other Article(s)
1
Bendzunas GN, Byrne DP, Shrestha S, Daly LA, Oswald SO, Katiyar S, Venkat A, Yeung W, Eyers CE, Eyers PA, Kannan N. Redox regulation and dynamic control of brain-selective kinases BRSK1/2 in the AMPK family through cysteine-based mechanisms. eLife 2025;13:RP92536. [PMID: 40172959 PMCID: PMC11964447 DOI: 10.7554/elife.92536] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2025]  Open
2
Tzvetkov J, Eyers CE, Eyers PA, Ramsbottom KA, Oswald SO, Harris JA, Sun Z, Deutsch EW, Jones AR. Searching for Sulfotyrosines (sY) in a HA(pY)STACK. J Proteome Res 2025;24:1250-1264. [PMID: 39907647 PMCID: PMC11894665 DOI: 10.1021/acs.jproteome.4c00907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2024] [Revised: 01/10/2025] [Accepted: 01/24/2025] [Indexed: 02/06/2025]
3
Lancaster NM, Sinitcyn P, Forny P, Peters-Clarke TM, Fecher C, Smith AJ, Shishkova E, Arrey TN, Pashkova A, Robinson ML, Arp N, Fan J, Hansen J, Galmozzi A, Serrano LR, Rojas J, Gasch AP, Westphall MS, Stewart H, Hock C, Damoc E, Pagliarini DJ, Zabrouskov V, Coon JJ. Fast and deep phosphoproteome analysis with the Orbitrap Astral mass spectrometer. Nat Commun 2024;15:7016. [PMID: 39147754 PMCID: PMC11327265 DOI: 10.1038/s41467-024-51274-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Accepted: 08/02/2024] [Indexed: 08/17/2024]  Open
4
Jadav R, Weiland F, Noordermeer SM, Carroll T, Gao Y, Wang J, Zhou H, Lamoliatte F, Toth R, Macartney T, Brown F, Hastie CJ, Alabert C, van Attikum H, Zenke F, Masson JY, Rouse J. Chemo-Phosphoproteomic Profiling with ATR Inhibitors Berzosertib and Gartisertib Uncovers New Biomarkers and DNA Damage Response Regulators. Mol Cell Proteomics 2024;23:100802. [PMID: 38880245 PMCID: PMC11338954 DOI: 10.1016/j.mcpro.2024.100802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 06/04/2024] [Accepted: 06/13/2024] [Indexed: 06/18/2024]  Open
5
Lancaster NM, Sinitcyn P, Forny P, Peters-Clarke TM, Fecher C, Smith AJ, Shishkova E, Arrey TN, Pashkova A, Robinson ML, Arp N, Fan J, Hansen J, Galmozzi A, Serrano LR, Rojas J, Gasch AP, Westphall MS, Stewart H, Hock C, Damoc E, Pagliarini DJ, Zabrouskov V, Coon JJ. Fast and Deep Phosphoproteome Analysis with the Orbitrap Astral Mass Spectrometer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.21.568149. [PMID: 38045259 PMCID: PMC10690147 DOI: 10.1101/2023.11.21.568149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
6
Bendzunas GN, Byrne DP, Shrestha S, Daly LA, Oswald SO, Katiyar S, Venkat A, Yeung W, Eyers CE, Eyers PA, Kannan N. Redox Regulation of Brain Selective Kinases BRSK1/2: Implications for Dynamic Control of the Eukaryotic AMPK family through Cys-based mechanisms. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.05.561145. [PMID: 38586025 PMCID: PMC10996518 DOI: 10.1101/2023.10.05.561145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
7
Wang B, Li Z, Shi Y, Zhu Z, Fields L, Shelef MA, Li L. Mass Spectrometry-Based Precise Identification of Citrullinated Histones via Limited Digestion and Biotin Derivative Tag Enrichment. Anal Chem 2024;96:2309-2317. [PMID: 38285917 PMCID: PMC11526168 DOI: 10.1021/acs.analchem.3c02646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2024]
8
Po A, Eyers CE. Top-Down Proteomics and the Challenges of True Proteoform Characterization. J Proteome Res 2023;22:3663-3675. [PMID: 37937372 PMCID: PMC10696603 DOI: 10.1021/acs.jproteome.3c00416] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 10/09/2023] [Accepted: 10/20/2023] [Indexed: 11/09/2023]
9
Daly L, Byrne DP, Perkins S, Brownridge PJ, McDonnell E, Jones AR, Eyers PA, Eyers CE. Custom Workflow for the Confident Identification of Sulfotyrosine-Containing Peptides and Their Discrimination from Phosphopeptides. J Proteome Res 2023;22:3754-3772. [PMID: 37939282 PMCID: PMC10696596 DOI: 10.1021/acs.jproteome.3c00425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 09/30/2023] [Accepted: 10/13/2023] [Indexed: 11/10/2023]
10
Rexhaj F, Sabel N, Robertson A, Lundgren T. Evaluation of method parameters for sound undecalcified dental enamel proteomics using liquid chromatography-mass spectrometry. Arch Oral Biol 2023;155:105802. [PMID: 37717379 DOI: 10.1016/j.archoralbio.2023.105802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 08/24/2023] [Accepted: 09/04/2023] [Indexed: 09/19/2023]
11
Venkat A, Watterson G, Byrne DP, O'Boyle B, Shrestha S, Gravel N, Fairweather EE, Daly LA, Bunn C, Yeung W, Aggarwal I, Katiyar S, Eyers CE, Eyers PA, Kannan N. Mechanistic and evolutionary insights into isoform-specific 'supercharging' in DCLK family kinases. eLife 2023;12:RP87958. [PMID: 37883155 PMCID: PMC10602587 DOI: 10.7554/elife.87958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2023]  Open
12
De La Toba EA, Anapindi KDB, Sweedler JV. Assessment and Comparison of Database Search Engines for Peptidomic Applications. J Proteome Res 2023;22:3123-3134. [PMID: 36809008 PMCID: PMC10440370 DOI: 10.1021/acs.jproteome.2c00307] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
13
Daly LA, Clarke CJ, Po A, Oswald SO, Eyers CE. Considerations for defining +80 Da mass shifts in mass spectrometry-based proteomics: phosphorylation and beyond. Chem Commun (Camb) 2023;59:11484-11499. [PMID: 37681662 PMCID: PMC10521633 DOI: 10.1039/d3cc02909c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 08/21/2023] [Indexed: 09/09/2023]
14
Carruthers NJ, Guo C, Gill R, Stemmer PM, Rosenspire AJ. Mercury intoxication disrupts tonic signaling in B cells, and may promote autoimmunity due to abnormal phosphorylation of STIM-1 and other autoimmunity risk associated phosphoproteins involved in BCR signaling. Toxicol Appl Pharmacol 2023;474:116607. [PMID: 37348680 PMCID: PMC10534200 DOI: 10.1016/j.taap.2023.116607] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 06/09/2023] [Accepted: 06/19/2023] [Indexed: 06/24/2023]
15
Tan KS, Azman AS, Hassandarvish P, Amelia-Yap ZH, Tan TK, Low VL. Protein Profiling of Aedes aegypti Treated with Streptomyces sp. KSF103 Ethyl Acetate Extract Reveals Potential Insecticidal Targets and Metabolic Pathways. Int J Mol Sci 2023;24:12398. [PMID: 37569772 PMCID: PMC10418484 DOI: 10.3390/ijms241512398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Revised: 06/27/2023] [Accepted: 06/30/2023] [Indexed: 08/13/2023]  Open
16
Venkat A, Watterson G, Byrne DP, O’Boyle B, Shrestha S, Gravel N, Fairweather EE, Daly LA, Bunn C, Yeung W, Aggarwal I, Katiyar S, Eyers CE, Eyers PA, Kannan N. Mechanistic and evolutionary insights into isoform-specific 'supercharging' in DCLK family kinases. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.29.534689. [PMID: 37034755 PMCID: PMC10081240 DOI: 10.1101/2023.03.29.534689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
17
Révész Á, Hevér H, Steckel A, Schlosser G, Szabó D, Vékey K, Drahos L. Collision energies: Optimization strategies for bottom-up proteomics. MASS SPECTROMETRY REVIEWS 2023;42:1261-1299. [PMID: 34859467 DOI: 10.1002/mas.21763] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 11/17/2021] [Accepted: 11/17/2021] [Indexed: 06/07/2023]
18
Zong Y, Wang Y, Yang Y, Zhao D, Wang X, Shen C, Qiao L. DeepFLR facilitates false localization rate control in phosphoproteomics. Nat Commun 2023;14:2269. [PMID: 37080984 PMCID: PMC10119288 DOI: 10.1038/s41467-023-38035-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 04/06/2023] [Indexed: 04/22/2023]  Open
19
Byrne DP, Shrestha S, Daly LA, Marensi V, Ramakrishnan K, Eyers CE, Kannan N, Eyers PA. Evolutionary and cellular analysis of the 'dark' pseudokinase PSKH2. Biochem J 2023;480:141-160. [PMID: 36520605 PMCID: PMC9988210 DOI: 10.1042/bcj20220474] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 12/12/2022] [Accepted: 12/15/2022] [Indexed: 12/23/2022]
20
Zhang J, Song H, Dong Y, Li G, Li J, Cai Q, Yuan S, Wang Y, Song H. Surface Engineering of HEK293 Cell-Derived Extracellular Vesicles for Improved Pharmacokinetic Profile and Targeted Delivery of IL-12 for the Treatment of Hepatocellular Carcinoma. Int J Nanomedicine 2023;18:209-223. [PMID: 36660339 PMCID: PMC9844138 DOI: 10.2147/ijn.s388916] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 12/24/2022] [Indexed: 01/14/2023]  Open
21
Gassaway BM, Li J, Rad R, Mintseris J, Mohler K, Levy T, Aguiar M, Beausoleil SA, Paulo JA, Rinehart J, Huttlin EL, Gygi SP. A multi-purpose, regenerable, proteome-scale, human phosphoserine resource for phosphoproteomics. Nat Methods 2022;19:1371-1375. [PMID: 36280721 PMCID: PMC9847208 DOI: 10.1038/s41592-022-01638-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 09/06/2022] [Indexed: 01/21/2023]
22
Hunter JE, Campbell AE, Kerridge S, Fraser C, Hannaway NL, Luli S, Ivanova I, Brownridge PJ, Coxhead J, Taylor L, Leary P, Hasoon MSR, Eyers CE, Perkins ND. Up-regulation of the PI3K/AKT and RHO/RAC/PAK signalling pathways in CHK1 inhibitor resistant Eµ-Myc lymphoma cells. Biochem J 2022;479:2131-2151. [PMID: 36240067 PMCID: PMC9704644 DOI: 10.1042/bcj20220103] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 09/19/2022] [Accepted: 09/20/2022] [Indexed: 12/14/2022]
23
Hunter JE, Campbell AE, Butterworth JA, Sellier H, Hannaway NL, Luli S, Floudas A, Kenneth NS, Moore AJ, Brownridge PJ, Thomas HD, Coxhead J, Taylor L, Leary P, Hasoon MS, Knight AM, Garrett MD, Collins I, Eyers CE, Perkins ND. Mutation of the RelA(p65) Thr505 phosphosite disrupts the DNA replication stress response leading to CHK1 inhibitor resistance. Biochem J 2022;479:2087-2113. [PMID: 36240065 PMCID: PMC9704643 DOI: 10.1042/bcj20220089] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 07/22/2022] [Accepted: 08/19/2022] [Indexed: 12/14/2022]
24
Hunter JE, Campbell AE, Hannaway NL, Kerridge S, Luli S, Butterworth JA, Sellier H, Mukherjee R, Dhillon N, Sudhindar PD, Shukla R, Brownridge PJ, Bell HL, Coxhead J, Taylor L, Leary P, Hasoon MS, Collins I, Garrett MD, Eyers CE, Perkins ND. Regulation of CHK1 inhibitor resistance by a c-Rel and USP1 dependent pathway. Biochem J 2022;479:2063-2086. [PMID: 36240066 PMCID: PMC9704646 DOI: 10.1042/bcj20220102] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 08/12/2022] [Accepted: 08/23/2022] [Indexed: 12/19/2022]
25
Omar MH, Byrne DP, Jones KN, Lakey TM, Collins KB, Lee KS, Daly LA, Forbush KA, Lau HT, Golkowski M, McKnight GS, Breault DT, Lefrançois-Martinez AM, Martinez A, Eyers CE, Baird GS, Ong SE, Smith FD, Eyers PA, Scott JD. Mislocalization of protein kinase A drives pathology in Cushing's syndrome. Cell Rep 2022;40:111073. [PMID: 35830806 PMCID: PMC9311266 DOI: 10.1016/j.celrep.2022.111073] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 04/20/2022] [Accepted: 06/17/2022] [Indexed: 01/15/2023]  Open
26
Piovesana S, Capriotti AL, Cavaliere C, Cerrato A, Montone CM, Zenezini Chiozzi R, Laganà A. The Key Role of Metal Adducts in the Differentiation of Phosphopeptide from Sulfopeptide Sequences by High-Resolution Mass Spectrometry. Anal Chem 2022;94:9234-9241. [PMID: 35714062 PMCID: PMC9260711 DOI: 10.1021/acs.analchem.1c05621] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 06/06/2022] [Indexed: 11/28/2022]
27
Mechanism of glycogen synthase inactivation and interaction with glycogenin. Nat Commun 2022;13:3372. [PMID: 35690592 PMCID: PMC9188544 DOI: 10.1038/s41467-022-31109-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 06/02/2022] [Indexed: 11/08/2022]  Open
28
Ramsbottom KA, Prakash A, Riverol YP, Camacho OM, Martin MJ, Vizcaíno JA, Deutsch EW, Jones AR. Method for Independent Estimation of the False Localization Rate for Phosphoproteomics. J Proteome Res 2022;21:1603-1615. [PMID: 35640880 PMCID: PMC9251759 DOI: 10.1021/acs.jproteome.1c00827] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
29
Kalyuzhnyy A, Eyers PA, Eyers CE, Bowler-Barnett E, Martin MJ, Sun Z, Deutsch EW, Jones AR. Profiling the Human Phosphoproteome to Estimate the True Extent of Protein Phosphorylation. J Proteome Res 2022;21:1510-1524. [PMID: 35532924 PMCID: PMC9171898 DOI: 10.1021/acs.jproteome.2c00131] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
30
Khanam T, Muñoz I, Weiland F, Carroll T, Morgan M, Borsos BN, Pantazi V, Slean M, Novak M, Toth R, Appleton P, Pankotai T, Zhou H, Rouse J. CDKL5 kinase controls transcription-coupled responses to DNA damage. EMBO J 2021;40:e108271. [PMID: 34605059 PMCID: PMC8634139 DOI: 10.15252/embj.2021108271] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 09/08/2021] [Accepted: 09/09/2021] [Indexed: 12/19/2022]  Open
31
Kulyyassov A, Fresnais M, Longuespée R. Targeted liquid chromatography-tandem mass spectrometry analysis of proteins: Basic principles, applications, and perspectives. Proteomics 2021;21:e2100153. [PMID: 34591362 DOI: 10.1002/pmic.202100153] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 09/08/2021] [Accepted: 09/24/2021] [Indexed: 12/25/2022]
32
Daly LA, Brownridge PJ, Batie M, Rocha S, Sée V, Eyers CE. Oxygen-dependent changes in binding partners and post-translational modifications regulate the abundance and activity of HIF-1α/2α. Sci Signal 2021;14:eabf6685. [PMID: 34285132 DOI: 10.1126/scisignal.abf6685] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
33
Campbell AE, Ferraz Franco C, Su LI, Corbin EK, Perkins S, Kalyuzhnyy A, Jones AR, Brownridge PJ, Perkins ND, Eyers CE. Temporal modulation of the NF-κB RelA network in response to different types of DNA damage. Biochem J 2021;478:533-551. [PMID: 33438746 PMCID: PMC7886319 DOI: 10.1042/bcj20200627] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 01/11/2021] [Accepted: 01/12/2021] [Indexed: 12/30/2022]
34
Use of the Polo-like kinase 4 (PLK4) inhibitor centrinone to investigate intracellular signalling networks using SILAC-based phosphoproteomics. Biochem J 2020;477:2451-2475. [PMID: 32501498 PMCID: PMC7338032 DOI: 10.1042/bcj20200309] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 05/27/2020] [Accepted: 06/05/2020] [Indexed: 12/22/2022]
35
Proceedings of the EuBIC-MS 2020 Developers’ Meeting. EUPA OPEN PROTEOMICS 2020. [DOI: 10.1016/j.euprot.2020.11.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
36
Yang Y, Horvatovich P, Qiao L. Fragment Mass Spectrum Prediction Facilitates Site Localization of Phosphorylation. J Proteome Res 2020;20:634-644. [PMID: 32985198 DOI: 10.1021/acs.jproteome.0c00580] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
37
Velázquez D, Albacar M, Zhang C, Calafí C, López-Malo M, Torres-Torronteras J, Martí R, Kovalchuk SI, Pinson B, Jensen ON, Daignan-Fornier B, Casamayor A, Ariño J. Yeast Ppz1 protein phosphatase toxicity involves the alteration of multiple cellular targets. Sci Rep 2020;10:15613. [PMID: 32973189 PMCID: PMC7519054 DOI: 10.1038/s41598-020-72391-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Accepted: 08/31/2020] [Indexed: 12/13/2022]  Open
38
Ultraviolet photodissociation of fondaparinux generates signature antithrombin-like 3-O-sulfated -GlcNS3S6S- monosaccharide fragment (Y3/C3). Anal Bioanal Chem 2020;412:7925-7935. [DOI: 10.1007/s00216-020-02925-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Revised: 07/27/2020] [Accepted: 08/28/2020] [Indexed: 12/22/2022]
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Locard-Paulet M, Bouyssié D, Froment C, Burlet-Schiltz O, Jensen LJ. Comparing 22 Popular Phosphoproteomics Pipelines for Peptide Identification and Site Localization. J Proteome Res 2020;19:1338-1345. [PMID: 31975593 DOI: 10.1021/acs.jproteome.9b00679] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Tomlinson LJ, Clubbs Coldron AKM, Eyers PA, Eyers CE. Determination of Phosphohistidine Stoichiometry in Histidine Kinases by Intact Mass Spectrometry. Methods Mol Biol 2020;2077:83-91. [PMID: 31707653 DOI: 10.1007/978-1-4939-9884-5_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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High-Throughput Characterization of Histidine Phosphorylation Sites Using UPAX and Tandem Mass Spectrometry. Methods Mol Biol 2020;2077:225-235. [PMID: 31707662 DOI: 10.1007/978-1-4939-9884-5_15] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Comprehensive Quantification of the Modified Proteome Reveals Oxidative Heart Damage in Mitochondrial Heteroplasmy. Cell Rep 2019;23:3685-3697.e4. [PMID: 29925008 DOI: 10.1016/j.celrep.2018.05.080] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 04/13/2018] [Accepted: 05/23/2018] [Indexed: 12/22/2022]  Open
43
Shteynberg DD, Deutsch EW, Campbell DS, Hoopmann MR, Kusebauch U, Lee D, Mendoza L, Midha MK, Sun Z, Whetton AD, Moritz RL. PTMProphet: Fast and Accurate Mass Modification Localization for the Trans-Proteomic Pipeline. J Proteome Res 2019;18:4262-4272. [PMID: 31290668 PMCID: PMC6898736 DOI: 10.1021/acs.jproteome.9b00205] [Citation(s) in RCA: 99] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
44
Hardman G, Perkins S, Brownridge PJ, Clarke CJ, Byrne DP, Campbell AE, Kalyuzhnyy A, Myall A, Eyers PA, Jones AR, Eyers CE. Strong anion exchange-mediated phosphoproteomics reveals extensive human non-canonical phosphorylation. EMBO J 2019;38:e100847. [PMID: 31433507 PMCID: PMC6826212 DOI: 10.15252/embj.2018100847] [Citation(s) in RCA: 111] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 07/24/2019] [Accepted: 08/01/2019] [Indexed: 12/18/2022]  Open
45
Zhang Z, Hebert AS, Westphall MS, Coon JJ, Dovichi NJ. Single-Shot Capillary Zone Electrophoresis-Tandem Mass Spectrometry Produces over 4400 Phosphopeptide Identifications from a 220 ng Sample. J Proteome Res 2019;18:3166-3173. [PMID: 31180221 DOI: 10.1021/acs.jproteome.9b00244] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
46
Zhang Y, Wen Z, Washburn MP, Florens L. Evaluating Chromatographic Approaches for the Quantitative Analysis of a Human Proteome on Orbitrap-Based Mass Spectrometry Systems. J Proteome Res 2019;18:1857-1869. [PMID: 30884231 DOI: 10.1021/acs.jproteome.9b00036] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
47
Lazar IM, Deng J, Stremler MA, Ahuja S. Microfluidic reactors for advancing the MS analysis of fast biological responses. MICROSYSTEMS & NANOENGINEERING 2019;5:7. [PMID: 31057934 PMCID: PMC6369226 DOI: 10.1038/s41378-019-0048-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 11/08/2018] [Accepted: 12/29/2018] [Indexed: 06/09/2023]
48
Potel C, Lemeer S, Heck AJR. Phosphopeptide Fragmentation and Site Localization by Mass Spectrometry: An Update. Anal Chem 2019;91:126-141. [PMID: 30457327 PMCID: PMC6322148 DOI: 10.1021/acs.analchem.8b04746] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Vonderach M, Byrne DP, Barran PE, Eyers PA, Eyers CE. DNA Binding and Phosphorylation Regulate the Core Structure of the NF-κB p50 Transcription Factor. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019;30:128-138. [PMID: 29873020 PMCID: PMC6318249 DOI: 10.1007/s13361-018-1984-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 04/26/2018] [Accepted: 04/30/2018] [Indexed: 05/07/2023]
50
Jones FK, Hardman GE, Ferries S, Eyers CE, Pisconti A. Myoblast Phosphoproteomics as a Tool to Investigate Global Signaling Events During Myogenesis. Methods Mol Biol 2019;1889:301-317. [PMID: 30367422 DOI: 10.1007/978-1-4939-8897-6_18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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