My Bibliography

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Li H, Smith BK, Mark L, Nemes P, Nazarian J, Vertes A. Ambient molecular imaging by laser ablation electrospray ionization mass spectrometry with ion mobility separation. International Journal of Mass Spectrometry. Forthcoming; 377(1):681. doi: 10.1016/j.ijms.2014.06.025.

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Pade LR, Lombard-Banek C, Li J, Nemes P. Dilute to Enrich for Deeper Proteomics: A Yolk-Depleted Carrier for Limited Populations of Embryonic (Frog) Cells. J Proteome Res. 2024 Feb 2;23(2):692-703. doi: 10.1021/acs.jproteome.3c00541. Epub 2023 Nov 23. PubMed PMID: 37994825; PubMed Central PMCID: PMC10872351.

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Pade LR, Stepler KE, Portero EP, DeLaney K, Nemes P. Biological mass spectrometry enables spatiotemporal 'omics: From tissues to cells to organelles. Mass Spectrom Rev. 2024 Jan-Feb;43(1):106-138. doi: 10.1002/mas.21824. Epub 2023 Jan 16. Review. PubMed PMID: 36647247; PubMed Central PMCID: PMC10668589.

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Choi SB, Vatan T, Alexander TA, Zhang C, Mitchell SM, Speer CM, Nemes P. Microanalytical Mass Spectrometry with Super-Resolution Microscopy Reveals a Proteome Transition During Development of the Brain's Circadian Pacemaker. Anal Chem. 2023 Oct 17;95(41):15208-15216. doi: 10.1021/acs.analchem.3c01987. Epub 2023 Oct 4. PubMed PMID: 37792996; PubMed Central PMCID: PMC10728713.

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Stepler KE, Hannah SC, Taneyhill LA, Nemes P. Deep Proteome of the Developing Chick Midbrain. J Proteome Res. 2023 Oct 6;22(10):3264-3274. doi: 10.1021/acs.jproteome.3c00291. Epub 2023 Aug 24. PubMed PMID: 37616547.

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Baxi AB, Nemes P, Moody SA. Time-resolved quantitative proteomic analysis of the developing Xenopus otic vesicle reveals putative congenital hearing loss candidates. iScience. 2023 Sep 15;26(9):107665. doi: 10.1016/j.isci.2023.107665. eCollection 2023 Sep 15. PubMed PMID: 37670778; PubMed Central PMCID: PMC10475516.

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Baxi AB, Li J, Quach VM, Nemes P. Cell Lineage-Guided Microanalytical Mass Spectrometry Reveals Increased Energy Metabolism and Reactive Oxygen Species in the Vertebrate Organizer. bioRxiv. 2023 Jul 9;. doi: 10.1101/2023.07.07.548174. PubMed PMID: 37461553; PubMed Central PMCID: PMC10350060.

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Gatto L, Aebersold R, Cox J, Demichev V, Derks J, Emmott E, Franks AM, Ivanov AR, Kelly RT, Khoury L, Leduc A, MacCoss MJ, Nemes P, Perlman DH, Petelski AA, Rose CM, Schoof EM, Van Eyk J, Vanderaa C, Yates JR 3rd, Slavov N. Initial recommendations for performing, benchmarking and reporting single-cell proteomics experiments. Nat Methods. 2023 Mar;20(3):375-386. doi: 10.1038/s41592-023-01785-3. Epub 2023 Mar 2. Review. PubMed PMID: 36864200; PubMed Central PMCID: PMC10130941.

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Portero EP, Pade L, Li J, Choi SB, Nemes P. Single-Cell Mass Spectrometry of Metabolites and Proteins for Systems and Functional Biology. Neuromethods. 2022;184:87-114. doi: 10.1007/978-1-0716-2525-5_5. Epub 2022 Aug 11. PubMed PMID: 36699808; PubMed Central PMCID: PMC9872963.

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DeLaney K, Jia D, Iyer L, Yu Z, Choi SB, Marvar PJ, Nemes P. Microanalysis of Brain Angiotensin Peptides Using Ultrasensitive Capillary Electrophoresis Trapped Ion Mobility Mass Spectrometry. Anal Chem. 2022 Jun 28;94(25):9018-9025. doi: 10.1021/acs.analchem.2c01062. Epub 2022 Jun 13. PubMed PMID: 35696295; PubMed Central PMCID: PMC9509539.

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Baxi AB, Pade LR, Nemes P. Cell-Lineage Guided Mass Spectrometry Proteomics in the Developing (Frog) Embryo. J Vis Exp. 2022 Apr 21;(182). doi: 10.3791/63586. PubMed PMID: 35532271; PubMed Central PMCID: PMC9513837.

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Shen B, Pade LR, Choi SB, Muñoz-LLancao P, Manzini MC, Nemes P. Capillary Electrophoresis Mass Spectrometry for Scalable Single-Cell Proteomics. Front Chem. 2022;10:863979. doi: 10.3389/fchem.2022.863979. eCollection 2022. PubMed PMID: 35464213; PubMed Central PMCID: PMC9024316.

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Choi SB, Polter AM, Nemes P. Patch-Clamp Proteomics of Single Neurons in Tissue Using Electrophysiology and Subcellular Capillary Electrophoresis Mass Spectrometry. Anal Chem. 2022 Jan 25;94(3):1637-1644. doi: 10.1021/acs.analchem.1c03826. Epub 2021 Dec 29. PubMed PMID: 34964611.

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Choi SB, Muñoz-LLancao P, Manzini MC, Nemes P. Data-Dependent Acquisition Ladder for Capillary Electrophoresis Mass Spectrometry-Based Ultrasensitive (Neuro)Proteomics. Anal Chem. 2021 Dec 7;93(48):15964-15972. doi: 10.1021/acs.analchem.1c03327. Epub 2021 Nov 23. PubMed PMID: 34812615.

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Nemes P. Mass spectrometry comes of age for subcellular organelles. Nature Methods. 2021 October; 18(10):1157-1158. doi: 10.1038/s41592-021-01287-0.

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Nemes P. Mass spectrometry comes of age for subcellular organelles. Nat Methods. 2021 Oct;18(10):1157-1158. doi: 10.1038/s41592-021-01287-0. PubMed PMID: 34608316.

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Choi S, Polter A, Nemes P. Patch-Clamp Proteomics of Single Neuronal Somas in Tissue Using Electrophysiology and Subcellular Capillary Electrophoresis Mass Spectrometry. [preprint]. 2021 September. doi: 10.1101/2021.09.02.458040.

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Choi S, Muñoz-LLancao P, Chiara Manzini M, Nemes P. A Data-Dependent Acquisition Ladder for Ultrasensitive (Neuro)Proteomics. [preprint]. 2021 August. doi: 10.1101/2021.08.03.454943.

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Lombard-Banek C, Li J, Portero EP, Onjiko RM, Singer CD, Plotnick DO, Al Shabeeb RQ, Nemes P. In Vivo Subcellular Mass Spectrometry Enables Proteo-Metabolomic Single-Cell Systems Biology in a Chordate Embryo Developing to a Normally Behaving Tadpole (X. laevis)*. Angew Chem Int Ed Engl. 2021 Jun 1;60(23):12852-12858. doi: 10.1002/anie.202100923. Epub 2021 Apr 8. PubMed PMID: 33682213; PubMed Central PMCID: PMC8176382.

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Onjiko RM, Nemes P, Moody SA. Altering metabolite distribution at Xenopus cleavage stages affects left-right gene expression asymmetries. Genesis. 2021 Jun;59(5-6):e23418. doi: 10.1002/dvg.23418. Epub 2021 Apr 7. PubMed PMID: 33826226; PubMed Central PMCID: PMC8943826.

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Baxi AB, Pade LR, Nemes P. Mass spectrometry based proteomics for developmental neurobiology in the amphibian Xenopus laevis. Curr Top Dev Biol. 2021;145:205-231. doi: 10.1016/bs.ctdb.2021.04.002. Epub 2021 May 25. Review. PubMed PMID: 34074530; PubMed Central PMCID: PMC8314003.

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Li J, Wu R, Yung M, Sun J, Li Z, Yang H, Zhang Y, Liu S, Cheung A, Ngan H, Braisted J, Zheng W, Wei H, Gao Y, Nemes P, Pei H, Chan D, Li Y, Zhu W. SENP1-mediated deSUMOylation of JAK2 regulates its kinase activity and platinum drug resistance. Cell Death & Disease. 2021 April; 12(4):-. doi: 10.1038/s41419-021-03635-6.

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Drouin N, van Mever M, Zhang W, Tobolkina E, Ferre S, Servais AC, Gou MJ, Nyssen L, Fillet M, Lageveen-Kammeijer GSM, Nouta J, Chetwynd AJ, Lynch I, Thorn JA, Meixner J, Lößner C, Taverna M, Liu S, Tran NT, Francois Y, Lechner A, Nehmé R, Al Hamoui Dit Banni G, Nasreddine R, Colas C, Lindner HH, Faserl K, Neusüß C, Nelke M, Lämmerer S, Perrin C, Bich-Muracciole C, Barbas C, Gonzálvez ÁL, Guttman A, Szigeti M, Britz-McKibbin P, Kroezen Z, Shanmuganathan M, Nemes P, Portero EP, Hankemeier T, Codesido S, González-Ruiz V, Rudaz S, Ramautar R. Capillary Electrophoresis-Mass Spectrometry at Trial by Metabo-Ring: Effective Electrophoretic Mobility for Reproducible and Robust Compound Annotation. Anal Chem. 2020 Oct 20;92(20):14103-14112. doi: 10.1021/acs.analchem.0c03129. Epub 2020 Oct 1. PubMed PMID: 32961048; PubMed Central PMCID: PMC7581015.

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Lombard-Banek C, Yu Z, Swiercz AP, Marvar PJ, Nemes P. Response to Letter to the Editor regarding "A microanalytical capillary electrophoresis mass spectrometry assay for quantifying angiotensin peptides in the brain". Anal Bioanal Chem. 2019 Dec;411(30):8165-8166. doi: 10.1007/s00216-019-02164-8. Epub 2019 Nov 20. PubMed PMID: 31745612; PubMed Central PMCID: PMC6923599.

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Danser AHJ, Poglitsch M. Letter to the Editor regarding "A microanalytical capillary electrophoresis mass spectrometry assay for quantifying angiotensin peptides in the brain". Anal Bioanal Chem. 2019 Dec;411(30):8163. doi: 10.1007/s00216-019-02162-w. Epub 2019 Nov 11. PubMed PMID: 31709469.

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Evers TMJ, Hochane M, Tans SJ, Heeren RMA, Semrau S, Nemes P, Mashaghi A. Deciphering Metabolic Heterogeneity by Single-Cell Analysis. Anal Chem. 2019 Nov 5;91(21):13314-13323. doi: 10.1021/acs.analchem.9b02410. Epub 2019 Oct 8. PubMed PMID: 31549807; PubMed Central PMCID: PMC6922888.

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Lombard-Banek C, Choi SB, Nemes P. Single-cell proteomics in complex tissues using microprobe capillary electrophoresis mass spectrometry. Methods Enzymol. 2019;628:263-292. doi: 10.1016/bs.mie.2019.07.001. Epub 2019 Aug 1. PubMed PMID: 31668233; PubMed Central PMCID: PMC7397975.

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Lombard-Banek C, Yu Z, Swiercz AP, Marvar PJ, Nemes P. A microanalytical capillary electrophoresis mass spectrometry assay for quantifying angiotensin peptides in the brain. Anal Bioanal Chem. 2019 Jul;411(19):4661-4671. doi: 10.1007/s00216-019-01771-9. Epub 2019 Apr 5. PubMed PMID: 30953113; PubMed Central PMCID: PMC6612282.

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Liu Z, Portero EP, Jian Y, Zhao Y, Onjiko RM, Zeng C, Nemes P. Trace, Machine Learning of Signal Images for Trace-Sensitive Mass Spectrometry: A Case Study from Single-Cell Metabolomics. Anal Chem. 2019 May 7;91(9):5768-5776. doi: 10.1021/acs.analchem.8b05985. Epub 2019 Apr 15. PubMed PMID: 30929422; PubMed Central PMCID: PMC6709531.

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Lombard-Banek C, Moody SA, Manzini MC, Nemes P. Microsampling Capillary Electrophoresis Mass Spectrometry Enables Single-Cell Proteomics in Complex Tissues: Developing Cell Clones in Live Xenopus laevis and Zebrafish Embryos. Anal Chem. 2019 Apr 2;91(7):4797-4805. doi: 10.1021/acs.analchem.9b00345. Epub 2019 Mar 18. PubMed PMID: 30827088; PubMed Central PMCID: PMC6688183.

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Portero EP, Nemes P. Dual cationic-anionic profiling of metabolites in a single identified cell in a live Xenopus laevis embryo by microprobe CE-ESI-MS. Analyst. 2019 Jan 28;144(3):892-900. doi: 10.1039/c8an01999a. PubMed PMID: 30542678; PubMed Central PMCID: PMC6349542.

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Baxi AB, Lombard-Banek C, Moody SA, Nemes P. Proteomic Characterization of the Neural Ectoderm Fated Cell Clones in the Xenopus laevis Embryo by High-Resolution Mass Spectrometry. ACS Chem Neurosci. 2018 Aug 15;9(8):2064-2073. doi: 10.1021/acschemneuro.7b00525. Epub 2018 Apr 5. PubMed PMID: 29578674; PubMed Central PMCID: PMC6093780.

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Onjiko RM, Portero EP, Nemes P. Single-cell metabolomics with capillary electrophoresis mass Spectrometry. In: Ramautar R, editor. Capillary Electrophoresis-Mass Spectrometry Approaches for Metabolomics in book: Royal Society of Chemistry; 2018. Chapter 4.

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Onjiko RM, Portero EP, Moody SA, Nemes P. Microprobe Capillary Electrophoresis Mass Spectrometry for Single-cell Metabolomics in Live Frog (Xenopus laevis) Embryos. J Vis Exp. 2017 Dec 22;(130). doi: 10.3791/56956. PubMed PMID: 29286491; PubMed Central PMCID: PMC5755674.

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Onjiko RM, Plotnick DO, Moody SA, Nemes P. Metabolic Comparison of Dorsal versus Ventral Cells Directly in the Live 8-cell Frog Embryo by Microprobe Single-cell CE-ESI-MS. Anal Methods. 2017 Sep 14;9(34):4964-4970. doi: 10.1039/C7AY00834A. Epub 2017 May 9. PubMed PMID: 29062391; PubMed Central PMCID: PMC5650250.

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Onjiko RM, Portero EP, Moody SA, Nemes P. In Situ Microprobe Single-Cell Capillary Electrophoresis Mass Spectrometry: Metabolic Reorganization in Single Differentiating Cells in the Live Vertebrate (Xenopus laevis) Embryo. Anal Chem. 2017 Jul 5;89(13):7069-7076. doi: 10.1021/acs.analchem.7b00880. Epub 2017 May 1. PubMed PMID: 28434226; PubMed Central PMCID: PMC5706767.

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Lombard-Banek C, Portero EP, Onjiko RM, Nemes P. New-generation mass spectrometry expands the toolbox of cell and developmental biology. Genesis. 2017 Jan;55(1-2). doi: 10.1002/dvg.23012. Review. PubMed PMID: 28095647; PubMed Central PMCID: PMC5276721.

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Choi S, Zamarbide M, Manzini M, Nemes P. Tapered-Tip Capillary Electrophoresis Nano-Electrospray Ionization Mass Spectrometry for Ultrasensitive Proteomics: the Mouse Cortex. Journal of the American Society for Mass Spectrometry. 2016 November; 28(4):597-607. doi: 10.1007/s13361-016-1532-8.

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Lombard-Banek C, Moody SA, Nemes P. High-Sensitivity Mass Spectrometry for Probing Gene Translation in Single Embryonic Cells in the Early Frog (Xenopus) Embryo. Front Cell Dev Biol. 2016;4:100. doi: 10.3389/fcell.2016.00100. eCollection 2016. PubMed PMID: 27761436; PubMed Central PMCID: PMC5050209.

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Onjiko RM, Morris SE, Moody SA, Nemes P. Single-cell mass spectrometry with multi-solvent extraction identifies metabolic differences between left and right blastomeres in the 8-cell frog (Xenopus) embryo. Analyst. 2016 Jun 21;141(12):3648-56. doi: 10.1039/c6an00200e. Epub 2016 Mar 23. PubMed PMID: 27004603; PubMed Central PMCID: PMC4899105.

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Lombard-Banek C, Moody SA, Nemes P. Single-Cell Mass Spectrometry for Discovery Proteomics: Quantifying Translational Cell Heterogeneity in the 16-Cell Frog (Xenopus) Embryo. Angew Chem Int Ed Engl. 2016 Feb 12;55(7):2454-8. doi: 10.1002/anie.201510411. Epub 2016 Jan 12. PubMed PMID: 26756663; PubMed Central PMCID: PMC4755155.

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Onjiko R, Morris S, Moody S, Nemes P. Single-cell mass spectrometry with multi-solvent extraction identifies metabolic differences between left and right blastomeres in the 8-cell frog (Xenopus) embryo. The Analyst. 2016; 141(12):3648-3656. doi: 10.1039/C6AN00200E.

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Li H, Wickramasekara S, Nemes P. One-hour screening of adulterated heparin by simplified peroxide digestion and fast RPIP-LC-MS(2). Anal Chem. 2015 Aug 18;87(16):8424-32. doi: 10.1021/acs.analchem.5b01788. Epub 2015 Jul 28. PubMed PMID: 26168275.

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Onjiko RM, Moody SA, Nemes P. Single-cell mass spectrometry reveals small molecules that affect cell fates in the 16-cell embryo. Proc Natl Acad Sci U S A. 2015 May 26;112(21):6545-50. doi: 10.1073/pnas.1423682112. Epub 2015 May 4. PubMed PMID: 25941375; PubMed Central PMCID: PMC4450407.

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Onjiko RM, Nemes P. Quantitative analysis of small molecules in single embryonic cells by microdissection single-cell CE-ESI-MS/MS. [Print]. Springer; 2015.

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Burton C, Guallar-Hoyas C, Li XJ, Nemes P, Shuhendler A. Announcing our finalists!. Bioanalysis. 2014;6(14):1883-8. doi: 10.4155/bio.14.183. Epub 2014 Jul 31. PubMed PMID: 25077522.

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Nemes P, Hoover WJ, Keire DA. High-throughput differentiation of heparin from other glycosaminoglycans by pyrolysis mass spectrometry. Anal Chem. 2013 Aug 6;85(15):7405-12. doi: 10.1021/ac401318q. Epub 2013 Jul 24. PubMed PMID: 23841449.

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Nemes P, Rubakhin SS, Aerts JT, Sweedler JV. Qualitative and quantitative metabolomic investigation of single neurons by capillary electrophoresis electrospray ionization mass spectrometry. Nat Protoc. 2013 Apr;8(4):783-99. doi: 10.1038/nprot.2013.035. Epub 2013 Mar 28. PubMed PMID: 23538882; PubMed Central PMCID: PMC3655804.

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Knolhoff AM, Nautiyal KM, Nemes P, Kalachikov S, Morozova I, Silver R, Sweedler JV. Combining small-volume metabolomic and transcriptomic approaches for assessing brain chemistry. Anal Chem. 2013 Mar 19;85(6):3136-43. doi: 10.1021/ac3032959. Epub 2013 Mar 1. PubMed PMID: 23409944; PubMed Central PMCID: PMC3605826.

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Nemes P, Knolhoff AM, Rubakhin SS, Sweedler JV. Single-cell metabolomics: changes in the metabolome of freshly isolated and cultured neurons. ACS Chem Neurosci. 2012 Oct 17;3(10):782-92. doi: 10.1021/cn300100u. Epub 2012 Aug 25. PubMed PMID: 23077722; PubMed Central PMCID: PMC3474288.