Proteomics - Key Publications Over the Last Five Years

1. Paraiso KH, Xiang Y, Rebecca VW, Abel EV, Chen YA, Munko AC, Wood E, Fedorenko IV, Sondak VK, Anderson AR, Ribas A, Palma MD, Nathanson KL, Koomen JM, Messina JL, Smalley KS. PTEN loss confers BRAF inhibitor resistance to melanoma cells through the suppression of BIM expression. Cancer Res 2011 Apr; 71: (7) 2750-2760 PMID: 21317224. PMCID: PMC3070772. IF: 9.329

2. Wong PG, Winter SL, Zaika E, Cao TV, Oguz U, Koomen JM, Hamlin JL, Alexandrow MG. Cdc45 limits replicon usage from a low density of preRCs in mammalian cells. PLoS One 2011 Jul; 6: (3) e17533- PMID: 21390258. PMCID: PMC3046982. IF: 3.234

3. Cross B, Chen L, Cheng Q, Li B, Yuan ZM, Chen J. Inhibition of p53 DNA binding function by the MDM2 protein acidic domain. J Biol Chem 2011 May; 286: (18) 16018-16029 PMID: 21454483. PMCID: PMC3091211. IF: 4.573

4. Permuth-Wey J, Chen Z, Tsai YY, Lin HY, Chen YA, Barnholtz-Sloan J, Birrer MJ, Chanock SJ, Cramer DW, Cunningham JM, Fenstermacher D, Fridley BL, Garcia-Closas M, Gayther SA, Gentry-Maharaj A, Gonzalez-Bosquet J, Iversen E, Jim H, McLaughlin J, Menon U, Narod SA, Phelan CM, Ramus SJ, Risch H, Song H, Sutphen R, Terry KL, Tyrer J, Vierkant RA, Wentzensen N, Lancaster JM, Cheng JQ, Berchuck A, Pharoah PD, Schildkraut JM, Goode EL, Sellers TA. MicroRNA processing and binding site polymorphisms are not replicated in the Ovarian Cancer Association Consortium. Cancer Epidemiol Biomarkers Prev 2011 Aug; 20: (8) 1793-1797 PMID: 21636674. PMCID: PMC3153581. IF: 4.125

5. Remily-Wood ER, Liu RZ, Xiang Y, Chen Y, Thomas CE, Rajyaguru N, Kaufman LM, Ochoa JE, Hazlehurst L, Pinilla-Ibarz J, Lancet J, Zhang G, Haura E, Shibata D, Yeatman T, Smalley KS, Dalton WS, Huang E, Scott E, Bloom GC, Eschrich SA, Koomen JM. A database of reaction monitoring mass spectrometry assays for elucidating therapeutic response in cancer. Proteom Clin Appl 2011 Aug; 5: (7-8) 383-396 PMID: 21656910. PMCID: PMC3530891. IF: 2.956

6. Guo JP, Coppola D, Cheng JQ. IKBKE protein activates Akt independent of phosphatidylinositol 3-kinase/PDK1/mTORC2 and the pleckstrin homology domain to sustain malignant transformation. J Biol Chem 2011 Oct; 286: (43) 37389-37398 PMID: 21908616. PMCID: PMC3199486.IF: 4.573

7. Martyniuk CJ, Fang B, Koomen JM, Gavin T, Zhang L, Barber DS, Lopachin RM. Molecular mechanism of glyceraldehyde-3-phosphate dehydrogenase inactivation by α,β-unsaturated carbonyl derivatives. Chem Res Toxicol 2011 Dec; 24: (12) 2302-2311 PMID: 22084934. PMCID: PMC3243798. IF: 3.529

8. Chang Y, Sun L, Kokura K, Horton JR, Fukuda M, Espejo A, Izumi V, Koomen JM, Bedford MT, Zhang X, Shinkai Y, Fang J, Cheng X. MPP8 mediates the interactions between DNA methyltransferase Dnmt3a and H3K9 methyltransferase GLP/G9a. Nat Commun 2012 May; 2: 533-PMID: 22086334. PMCID: PMC3286832. IF: 11.470

9. An Z, Chen Y, Koomen JM, Merkler DJ. A mass spectrometry-based method to screen for α-amidated peptides. Proteomics 2012 Jan; 12: (2) 173-182 PMID: 22106059. PMCID: PMC3517110. IF: 3.807

10. Ge Y, Kazi A, Marsilio F, Luo Y, Jain S, Brooks W, Daniel KG, Guida WC, Sebti SM, Lawrence HR. Discovery and synthesis of hydronaphthoquinones as novel proteasome inhibitors. J Med Chem 2012 Mar; 55: (5) 1978-1998 PMID: 22220566. PMCID: PMC3530929. IF: 5.447  

11. Xiang Y, Koomen JM. Evaluation of direct infusion-multiple reaction monitoring mass spectrometry for quantification of heat shock proteins. Anal Chem 2012 Feb; 84: (4) 1981-1986 PMID: 22293045. PMCID: PMC3332078. IF: 5.636

12. Guo J, Kim D, Gao J, Kurtyka C, Chen H, Yu C, Wu D, Mittal A, Beg AA, Chellappan SP, Haura EB, Cheng JQ. IKBKE is induced by STAT3 and tobacco carcinogen and determines chemosensitivity in non-small cell lung cancer. Oncogene 2013 Jan; 32: (2) 151-159 PMID: 22330135.PMCID: PMC4109158. IF: 8.459  

13. Park S, Kim D, Dan HC, Chen H, Testa JR, Cheng JQ. Identification of Akt interaction protein PHF20/TZP that transcriptionally regulates p53. J Biol Chem 2012 Mar; 287: (14) 11151-11163 PMID: 22334668. PMCID: PMC3322870. IF: 4.573

14. Paraiso KH, Haarberg HE, Wood E, Rebecca VW, Chen YA, Xiang Y, Ribas A, Lo RS, Weber JS, Sondak VK, John JK, Sarnaik AA, Koomen JM, Smalley KS. The HSP90 inhibitor XL888 overcomes BRAF inhibitor resistance mediated through diverse mechanisms. Clin Cancer Res 2012 May; 18: (9) 2502-2514 PMID: 22351686. PMCID: PMC3398738. IF: 8.722

15. Remily-Wood ER, Koomen JM. Evaluation of protein quantification using standard peptides containing single conservative amino acid replacements. J Mass Spectrom 2012 Feb; 47: (2) 188-194 PMID: 22359328. PMCID: PMC3465614. IF: 2.379

16. Wilson DS, Fang B, Dalton WS, Meade CD, Koomen JM. An ET-CURE pilot project supporting undergraduate training in cancer research, emerging technology, and health disparities. J Cancer Educ 2012 Jun; 27: (3) 418-427 PMID: 22528637. PMCID: PMC3439555. IF: 1.230  

17. Lawrence HR, Martin MP, Luo Y, Pireddu R, Yang H, Gevariya H, Ozcan S, Zhu JY, Kendig R, Rodriguez M, Elias R, Cheng JQ, Sebti SM, Schonbrunn E, Lawrence NJ. Development of o-chlorophenyl substituted pyrimidines as exceptionally potent aurora kinase inhibitors. J Med Chem2012 Sep; 55: (17) 7392-7416 PMID: 22803810. PMCID: PMC4429609. IF: 5.447

18. Cui G, Park S, Badeaux AI, Kim D, Lee J, Thompson JR, Yan F, Kaneko S, Yuan Z, Botuyan MV, Bedford MT, Cheng JQ, Mer G. PHF20 is an effector protein of p53 double lysine methylation that stabilizes and activates p53. Nat Struct Mol Biol 2012 Sep; 19: (9) 916-924 PMID: 22864287. PMCID: PMC3454513. IF: 13.309  

19. Mahajan K, Fang B, Koomen JM, Mahajan NP. H2B Tyr37 phosphorylation suppresses expression of replication-dependent core histone genes. Nat Struct Mol Biol 2012 Sep; 19: (9) 930-937 PMID: 22885324. PMCID: PMC4533924. IF: 13.309

20. Xu CX, Xu M, Tan L, Yang H, Permuth-Wey J, Kruk PA, Wenham RM, Nicosia SV, Lancaster JM, Sellers TA, Cheng JQ. MicroRNA miR-214 regulates ovarian cancer cell stemness by targeting p53/Nanog. J Biol Chem 2012 Oct; 287: (42) 34970-34978 PMID: 22927443. PMCID: PMC3471722. IF: 4.573  

21. Woods NT, Mesquita RD, Sweet M, Carvalho MA, Li X, Liu Y, Nguyen H, Thomas CE, Iversen ES, Marsillac S, Karchin R, Koomen J, Monteiro AN. Charting the landscape of tandem BRCT domain-mediated protein interactions. Sci Signal 2013 Feb; 5: (242) rs6- PMID: 22990118.PMCID: PMC4064718. IF: 6.279

22. Haarberg HE, Paraiso KH, Wood E, Rebecca VW, Sondak VK, Koomen JM, Smalley KS. Inhibition of Wee1, AKT, and CDK4 underlies the efficacy of the HSP90 inhibitor XL888 in an in vivo model of NRAS-mutant melanoma. Mol Cancer Ther 2013 Jun; 12: (6) 901-912 PMID: 23538902. PMCID: PMC3683468. IF: 5.683

23. Ozcan S, Kazi A, Marsilio F, Fang B, Guida WC, Koomen J, Lawrence HR, Sebti SM. Oxadiazole-isopropylamides as potent and noncovalent proteasome inhibitors. J Med Chem 2013 May; 56: (10) 3783-3805 PMID: 23547706. PMCID: PMC3774303. IF: 5.447

24. Martyniuk CJ, Feswick A, Fang B, Koomen JM, Barber DS, Gavin T, Lopachin RM. Protein targets of acrylamide adduct formation in cultured rat dopaminergic cells. Toxicol Lett 2013 Jun; 219: (3) 279-287 PMID: 23566896. PMCID: PMC3707521. IF: 3.262

25. Song T, Yang L, Kabra N, Chen L, Koomen J, Haura EB, Chen J. The NAD+ synthesis enzyme nicotinamide mononucleotide adenylyltransferase (NMNAT1) regulates ribosomal RNA transcription. J Biol Chem 2013 Jul; 288: (29) 20908-20917 PMID: 23737528. PMCID: PMC3774361.IF: 4.573

26. Kim JY, Welsh EA, Oguz U, Fang B, Bai Y, Kinose F, Bronk C, Remsing Rix LL, Beg AA, Rix U, Eschrich SA, Koomen JM, Haura EB. Dissection of TBK1 signaling via phosphoproteomics in lung cancer cells. Proc Natl Acad Sci U S A 2013 Jul; 110: (30) 12414-12419 PMID: 23836654. PMCID: PMC3725062. IF: 9.674

27. Gebhard AW, Jain P, Nair RR, Emmons MF, Argilagos RF, Koomen JM, McLaughlin ML, Hazlehurst LA. MTI-101 (cyclized HYD1) binds a CD44 containing complex and induces necrotic cell death in multiple myeloma. Mol Cancer Ther 2013 Nov; 12: (11) 2446-2458 PMID: 24048737.PMCID: PMC3859963. IF: 5.683  

28. Williams KA, Zhang M, Xiang S, Hu C, Wu JY, Zhang S, Ryan M, Cox AD, Der CJ, Fang B, Koomen J, Haura E, Bepler G, Nicosia SV, Matthias P, Wang C, Bai W, Zhang X. Extracellular signal-regulated kinase (ERK) phosphorylates histone deacetylase 6 (HDAC6) at serine 1035 to stimulate cell migration. J Biol Chem 2013 Nov; 288: (46) 33156-33170 PMID: 24089523. PMCID: PMC3829163. IF: 4.573

29. Zheng H, Yang L, Peng L, Izumi V, Koomen J, Seto E, Chen J. hMOF acetylation of DBC1/CCAR2 prevents binding and inhibition of SirT1. Mol Cell Biol 2013 Dec; 33: (24) 4960-4970 PMID: 24126058. PMCID: PMC3889553. IF: 4.777

30. Pierce Campbell CM, Guan W, Sprung R, Koomen JM, O'Keefe MT, Ingles DJ, Abrahamsen M, Giuliano AR. Quantification of secretory leukocyte protease inhibitor (SLPI) in oral gargle specimens collected using mouthwash. J Immunol Methods 2013 Dec; 400-401: 117-121 PMID: 24140751. PMCID: PMC3990009. IF: 1.820  

31. Zheng XQ, Guo JP, Yang H, Kanai M, He LL, Li YY, Koomen JM, Minton S, Gao M, Ren XB, Coppola D, Cheng JQ. Aurora-A is a determinant of tamoxifen sensitivity through phosphorylation of ERα in breast cancer. Oncogene 2014 Oct; 33: (42) 4985-4996 PMID: 24166501. PMCID: PMC4002670. IF: 8.459

32. Li J, Bennett K, Stukalov A, Fang B, Zhang G, Yoshida T, Okamoto I, Kim JY, Song L, Bai Y, Qian X, Rawal B, Schell M, Grebien F, Winter G, Rix U, Eschrich S, Colinge J, Koomen J, Superti-Furga G, Haura EB. Perturbation of the mutated EGFR interactome identifies vulnerabilities and resistance mechanisms. Mol Syst Biol 2014 Mar; 9: 705- PMID: 24189400. PMCID: PMC4039310. IF: 10.872

33. Remsing Rix LL, Kuenzi BM, Luo Y, Remily-Wood E, Kinose F, Wright G, Li J, Koomen JM, Haura EB, Lawrence HR, Rix U. GSK3 alpha and beta are new functionally relevant targets of tivantinib in lung cancer cells. Acs Chem Biol 2014 Feb; 9: (2) 353-358 PMID: 24215125. PMCID: PMC3944088. IF: 5.331

34. Kazi A, Ozcan S, Tecleab A, Sun Y, Lawrence HR, Sebti SM. Discovery of PI-1840, a novel noncovalent and rapidly reversible proteasome inhibitor with anti-tumor activity. J Biol Chem 2014 Apr; 289: (17) 11906-11915 PMID: 24570003. PMCID: PMC4002098. IF: 4.573  

35. Remily-Wood ER, Benson K, Baz RC, Chen YA, Hussein M, Hartley-Brown MA, Sprung RW, Perez B, Liu RZ, Yoder S, Teer J, Eschrich SA, Koomen JM. Quantification of peptides from immunoglobulin constant and variable regions by LC-MRM MS for assessment of multiple myeloma patients. Proteom Clin Appl 2014 Oct; 8: (9-10) 783-795 PMID: 24723328. PMCID: PMC4302417. IF: 2.956

36. Rebecca VW, Wood ER, Fedorenko IV, Paraiso KH, Haarberg HE, Chen Y, Xiang Y, Sarnaik A, Gibney GT, Sondak VK, Koomen JM, Smalley KS. Evaluating melanoma drug response and therapeutic escape with quantitative proteomics. Mol Cell Proteomics 2014 Jul; 13: (7) 1844-1854 PMID: 24760959. PMCID: PMC4083119. IF: 6.564

37. Zhang M, Xiang S, Joo HY, Wang L, Williams KA, Liu W, Hu C, Tong D, Haakenson J, Wang C, Zhang S, Pavlovicz RE, Jones A, Schmidt KH, Tang J, Dong H, Shan B, Fang B, Radhakrishnan R, Glazer PM, Matthias P, Koomen J, Seto E, Bepler G, Nicosia SV, Chen J, Li C, Gu L, Li GM, Bai W, Wang H, Zhang X. HDAC6 deacetylates and ubiquitinates MSH2 to maintain proper levels of MutSα. Mol Cell 2014 Jul; 55: (1) 31-46 PMID: 24882211. PMCID: PMC4188514. IF: 14.018

38. Yoshida T, Zhang G, Smith MA, Lopez AS, Bai Y, Li J, Fang B, Koomen JM, Rawal B, Fisher KJ, Chen YA, Kitano M, Morita Y, Yamaguchi H, Shibata K, Okabe T, Okamoto I, Nakagawa K, Haura EB. Tyrosine phosphoproteomics identifies both codrivers and cotargeting strategies for T790M-related EGFR-TKI resistance in non-small cell lung cancer. Clin Cancer Res 2014 Aug; 20: (15) 4059-4074 PMID: 24919575. PMCID: PMC4119578. IF: 8.722

39. Koomen JM. Immunoglobulins: expanding the role for mass spectrometry in protein biomarker quantification. Clin Chem 2014 Aug; 60: (8) 1034-1035 PMID: 24938750. PMCID: PMC4674789. IF: 7.911

40. Fedorenko IV, Fang B, Koomen JM, Gibney GT, Smalley KS. Amuvatinib has cytotoxic effects against NRAS-mutant melanoma but not BRAF-mutant melanoma. Melanoma Res 2014 Oct; 24: (5) 448-453 PMID: 24950457. PMCID: PMC4384823. IF: 2.282  

41. Fedorenko IV, Fang B, Munko AC, Gibney GT, Koomen JM, Smalley KS. Phosphoproteomic analysis of basal and therapy-induced adaptive signaling networks in BRAF and NRAS mutant melanoma. Proteomics 2015 Jan; 15: (2-3) 327-339 PMID: 25339196. PMCID: PMC4389901. IF: 3.807

42. Bai Y, Kim JY, Watters JM, Fang B, Kinose F, Song L, Koomen JM, Teer JK, Fisher K, Chen YA, Rix U, Haura EB. Adaptive responses to dasatinib-treated lung squamous cell cancer cells harboring DDR2 mutations. Cancer Res 2014 Dec; 74: (24) 7217-7228 PMID: 25348954. PMCID: PMC4326029. IF: 9.329

43. Paraiso KH, Thakur MD, Fang B, Koomen JM, Fedorenko IV, John JK, Tsao H, Flaherty KT, Sondak VK, Messina JL, Pasquale EB, Villagra A, Rao UN, Kirkwood JM, Meier F, Sloot S, Gibney GT, Stuart D, Tawbi H, Smalley KS. Ligand-independent EPHA2 signaling drives the adoption of a targeted therapy-mediated metastatic melanoma phenotype. Cancer Discov 2015 Mar; 5: (3) 264-273 PMID: 25542447. PMCID: PMC4355213. IF: 19.453

44. Yuan W, Sanda M, Wu J, Koomen J, Goldman R. Quantitative analysis of immunoglobulin subclasses and subclass specific glycosylation by LC-MS-MRM in liver disease. J Proteomics 2015 Feb; 116: 24-33 PMID: 25582524. PMCID: PMC4329072. IF: 3.888  

45. Richards EJ, Zhang G, Li ZP, Permuth-Wey J, Challa S, Li Y, Kong W, Dan S, Bui M, Coppola D, Mao WM, Sellers TA, Cheng JQ. Long non-coding RNAs (LncRNA) regulated by transforming growth factor (TGF) β: LncRNA-hit-mediated TGFβ-induced epithelial to mesenchymal transition in mammary epithelia. J Biol Chem 2015 Mar; 290: (11) 6857-6867 PMID: 25605728. PMCID: PMC4358111. IF: 4.573

46. Sun L, Kokura K, Izumi V, Koomen JM, Seto E, Chen J, Fang J. MPP8 and SIRT1 crosstalk in E-cadherin gene silencing and epithelial-mesenchymal transition. EMBO Rep 2015 Jun; 16: (6) 689-699 PMID: 25870236. PMCID: PMC4467853. IF: 9.055

47. Meads MB, Fang B, Mathews L, Gemmer J, Nong L, Rosado-Lopez I, Nguyen T, Ring JE, Matsui W, MacLeod AR, Pachter JA, Hazlehurst LA, Koomen JM, Shain KH. Targeting PYK2 mediates microenvironment-specific cell death in multiple myeloma. Oncogene 2015 Sep; In PressPMID: 26387544. PMCID: PMC4801703. IF: 8.459

48. Carr SA, Abbatiello SE, Ackermann BL, Borchers C, Domon B, Deutsch EW, Grant RP, Hoofnagle AN, H Uumlttenhain R, Koomen JM, Liebler DC, Liu T, Maclean B, Mani DR, Mansfield E, Neubert H, Paulovich AG, Reiter L, Vitek O, Aebersold R, Anderson L, Bethem R, Blonder J, Boja E, Botelho J, Boyne M, Bradshaw RA, Burlingame AL, Chan D, Keshishian H, Kuhn E, Kinsinger C, Lee J, Lee SW, Moritz R, Oses-Prieto J, Rifai N, Ritchie J, Rodriguez H, Srinivas PR, Townsend RR, Van Eyk J, Whiteley G, Wiita A, Weintraub S. Targeted peptide measurements in biology and medicine: best practices for mass spectrometry-based assay development using a fit-for-purpose approach. Mol Cell Proteomics 2014 Mar; 13: (3) 907-917 PMID: 24443746. PMCID: PMC3945918. IF: 6.564