Research

Mass Spectrometry Proteomics Core Publications

Master
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Key Technology Publications:

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Mindikoglu AL, Abdulsada MM, Jain A, Choi JM, Jalal PK, Devaraj S, Mezzari MP, Petrosino JF, Opekun AR, Jung SY. Intermittent fasting from dawn to sunset for 30 consecutive days is associated with anticancer proteomic signature and upregulates key regulatory proteins of glucose and lipid metabolism, circadian clock, DNA repair, cytoskeleton remodeling, immune system and cognitive function in healthy subjects. J Proteomics. 2020

Chen Y, Leng M, Gao Y, Zhan D, Choi JM, Song L, Li K, Xia X, Zhang C, Liu M, Ji S, Jain A, Saltzman AB, Malovannaya A, Qin J, Jung SY, Wang Y. A Cross-Linking-Aided Immunoprecipitation/Mass Spectrometry Workflow Reveals Extensive Intracellular Trafficking in Time-Resolved, Signal-Dependent Epidermal Growth Factor Receptor Proteome. J Proteome Res. 2019

Saltzman AB, Leng M, Bhatt B, Singh P, Chan DW, Dobrolecki L, Chandrasekaran  H, Choi JM, Jain A, Jung SY, Lewis MT, Ellis MJ, Malovannaya A. gpGrouper: A Peptide Grouping Algorithm for Gene-Centric Inference and Quantitation of Bottom-Up Proteomics Data. Molecular & Cellular Proteomics. 2018

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Other publications (selected):

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2022

Sardar D, Chen HC, Reyes A, Varadharajan S, Jain A, Mohila C, Curry R, Lozzi B, Rajendran K, Cervantes A, Yu K, Jalali A, Rao G, Mack SC, Deneen B. Sox9 directs divergent epigenomic states in brain tumor subtypes. Proc Natl Acad Sci USA. 2022 Jul 19;119(29):e2202015119. doi: 10.1073/pnas.2202015119. Epub 2022 Jul 15. 

Angelini A, Ortiz-Urbina J, Trial J, Reddy AK, Malovannaya A, Jain A, Entman ML, Taffet GE, Cieslik KA. Sex-specific phenotypes in the aging mouse heart and consequences for chronic fibrosis. Am J Physiol Heart Circ Physiol. 2022 Aug 1; 323(2):H285-H300.

Chern T, Achilleos A, Tong X, Hill MC, Saltzman AB, Reineke LC, Chaudhury A, Dasgupta SK, Redhead Y, Watkins D, Neilson JR, Thiagarajan P, Green JBA, Malovannaya A, Martin JF, Rosenblatt DS, Poché RA. Mutations in Hcfc1 and Ronin result in an inborn error of cobalamin metabolism and ribosomopathy. Nat Commun. 2022 Jan 10;13(1):134. doi: 10.1038/s41467-021-27759-7.. 

2021

Matrone G, Jung SY, Choi JM, Jain A, Leung HE, Rajapakshe K, Coarfa C, Rodor J, Denvir MA, Baker AH, Cooke JP. Nuclear S-nitrosylation impacts tissue regeneration in zebrafish. Nat Commun. 2021 Nov 1;12(1):6282. doi: 10.1038/s41467-021-26621-0

Matinyan N, Karkhanis MS, Gonzalez Y, Jain A, Saltzman A, Malovannaya A, Sarrion-Perdigones A, Dierick HA, Venken KJT. Multiplexed drug-based selection and counterselection genetic manipulations in Drosophila. Cell Rep. 2021 Sep 14;36(11):109700.

Bowling EA, Wang JH, Gong F, Wu W, Neill NJ, Kim IS, Tyagi S, Orellana M, Kurley SJ, Dominguez-Vidaña R, Chung HC, Hsu TY, Dubrulle J, Saltzman AB, Li H, Meena JK, Canlas GM, Chamakuri S, Singh S, Simon LM, Olson CM, Dobrolecki LE, Lewis MT, Zhang B, Golding I, Rosen JM, Young DW, Malovannaya A, Stossi F, Miles G, Ellis MJ, Yu L, Buonamici S, Lin CY, Karlin KL, Zhang XH, Westbrook TF. Spliceosome-targeted therapies trigger an antiviral immune response in triple- negative breast cancer. Cell. 2021 Jan 21;184(2):384-403.e21.

2020

Mindikoglu AL, Abdulsada MM, Jain A, Jalal PK, Devaraj S, Wilhelm ZR, Opekun AR, Jung SY. Intermittent fasting from dawn to sunset for four consecutive weeks induces anticancer serum proteome response and improves metabolic syndrome. Sci Rep. 2020 Oct 27;10(1):18341.

Li K, Jain A, Malovannaya A, Wen B, Zhang B. DeepRescore: Leveraging Deep Learning to Improve Peptide Identification in Immunopeptidomics. Proteomics. 2020 Nov;20(21-22):e1900334.

Satpathy S, Jaehnig EJ, Krug K, Kim BJ, Saltzman AB, Chan DW, Holloway KR, Anurag M, Huang C, Singh P, Gao A, Namai N, Dou Y, Wen B, Vasaikar SV, Mutch D, Watson MA, Ma C, Ademuyiwa FO, Rimawi MF, Schiff R, Hoog J, Jacobs S, Malovannaya A, Hyslop T, Clauser KR, Mani DR, Perou CM, Miles G, Zhang B, Gillette MA, Carr SA, Ellis MJ. Microscaled proteogenomic methods for precision oncology. Nat Commun. 2020 Jan 27;11(1):532.