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Mass spectrometry for translational proteomics: progress and clinical implications.

Genome medicine

Baker ES, Liu T, Petyuk VA, Burnum-Johnson KE, Ibrahim YM, Anderson GA, Smith RD.
PMID: 22943415
Genome Med. 2012 Aug 31;4(8):63. doi: 10.1186/gm364. eCollection 2012.

The utility of mass spectrometry (MS)-based proteomic analyses and their clinical applications have been increasingly recognized over the past decade due to their high sensitivity, specificity and throughput. MS-based proteomic measurements have been used in a wide range of...

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Baker ES, Liu T, Petyuk VA, et al. Mass spectrometry for translational proteomics: progress and clinical implications. Genome Med. 2012;4(8):63doi: 10.1186/gm364.
Baker, E. S., Liu, T., Petyuk, V. A., Burnum-Johnson, K. E., Ibrahim, Y. M., Anderson, G. A., & Smith, R. D. (2012). Mass spectrometry for translational proteomics: progress and clinical implications. Genome medicine, 4(8), 63. https://doi.org/10.1186/gm364
Baker, Erin Shammel, et al. "Mass spectrometry for translational proteomics: progress and clinical implications." Genome medicine vol. 4,8 (2012): 63. doi: https://doi.org/10.1186/gm364
Baker ES, Liu T, Petyuk VA, Burnum-Johnson KE, Ibrahim YM, Anderson GA, Smith RD. Mass spectrometry for translational proteomics: progress and clinical implications. Genome Med. 2012 Aug 31;4(8):63. doi: 10.1186/gm364. eCollection 2012. PMID: 22943415; PMCID: PMC3580401.
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Trapping a Photoelectron behind a Repulsive Coulomb Barrier in Solution.

The journal of physical chemistry letters

Cheng M, Rivas N, Lim SJ, Pichugin K, Petruk AA, Klinkova A, Smith R, Hopkins WS, Sciaini G.
PMID: 31498643
J Phys Chem Lett. 2019 Oct 03;10(19):5742-5747. doi: 10.1021/acs.jpclett.9b01712. Epub 2019 Sep 16.

Multiply charged anions (MCAs) display unique photophysics and solvent-stabilizing effects. Well-known aqueous species such as SO

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Cheng M, Rivas N, Lim SJ, et al. Trapping a Photoelectron behind a Repulsive Coulomb Barrier in Solution. J Phys Chem Lett. 2019;10(19):5742-5747doi: 10.1021/acs.jpclett.9b01712.
Cheng, M., Rivas, N., Lim, S. J., Pichugin, K., Petruk, A. A., Klinkova, A., Smith, R., Hopkins, W. S., & Sciaini, G. (2019). Trapping a Photoelectron behind a Repulsive Coulomb Barrier in Solution. The journal of physical chemistry letters, 10(19), 5742-5747. https://doi.org/10.1021/acs.jpclett.9b01712
Cheng, Meixin, et al. "Trapping a Photoelectron behind a Repulsive Coulomb Barrier in Solution." The journal of physical chemistry letters vol. 10,19 (2019): 5742-5747. doi: https://doi.org/10.1021/acs.jpclett.9b01712
Cheng M, Rivas N, Lim SJ, Pichugin K, Petruk AA, Klinkova A, Smith R, Hopkins WS, Sciaini G. Trapping a Photoelectron behind a Repulsive Coulomb Barrier in Solution. J Phys Chem Lett. 2019 Oct 03;10(19):5742-5747. doi: 10.1021/acs.jpclett.9b01712. Epub 2019 Sep 16. PMID: 31498643.
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Optimization of Biomass Accumulation and Production of Phenolic Compounds in Callus Cultures of .

Plants (Basel, Switzerland)

Erst AA, Petruk AA, Erst AS, Krivenko DA, Filinova NV, Maltseva SY, Kulikovskiy MS, Banaev EV.
PMID: 35009127
Plants (Basel). 2022 Jan 02;11(1). doi: 10.3390/plants11010124.

No abstract available.

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Erst AA, Petruk AA, Erst AS, et al. Optimization of Biomass Accumulation and Production of Phenolic Compounds in Callus Cultures of . Plants (Basel). 2022;11(1)doi: 10.3390/plants11010124.
Erst, A. A., Petruk, A. A., Erst, A. S., Krivenko, D. A., Filinova, N. V., Maltseva, S. Y., Kulikovskiy, M. S., & Banaev, E. V. (2022). Optimization of Biomass Accumulation and Production of Phenolic Compounds in Callus Cultures of . Plants (Basel, Switzerland), 11(1), . https://doi.org/10.3390/plants11010124
Erst, Anna A, et al. "Optimization of Biomass Accumulation and Production of Phenolic Compounds in Callus Cultures of ." Plants (Basel, Switzerland) vol. 11,1 (2022). doi: https://doi.org/10.3390/plants11010124
Erst AA, Petruk AA, Erst AS, Krivenko DA, Filinova NV, Maltseva SY, Kulikovskiy MS, Banaev EV. Optimization of Biomass Accumulation and Production of Phenolic Compounds in Callus Cultures of . Plants (Basel). 2022 Jan 02;11(1). doi: 10.3390/plants11010124. PMID: 35009127; PMCID: PMC8747766.
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The genetics of circulating BDNF: towards understanding the role of BDNF in brain structure and function in middle and old ages.

Brain communications

Li S, Weinstein G, Zare H, Teumer A, Völker U, Friedrich N, Knol MJ, Satizabal CL, Petyuk VA, Adams HHH, Launer LJ, Bennett DA, De Jager PL, Grabe HJ, Ikram MA, Gudnason V, Yang Q, Seshadri S.
PMID: 33345186
Brain Commun. 2020 Oct 28;2(2):fcaa176. doi: 10.1093/braincomms/fcaa176. eCollection 2020.

Brain-derived neurotrophic factor (BDNF) plays an important role in brain development and function. Substantial amounts of BDNF are present in peripheral blood, and may serve as biomarkers for Alzheimer's disease incidence as well as targets for intervention to reduce...

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Li S, Weinstein G, Zare H, et al. The genetics of circulating BDNF: towards understanding the role of BDNF in brain structure and function in middle and old ages. Brain Commun. 2020;2(2):fcaa176doi: 10.1093/braincomms/fcaa176.
Li, S., Weinstein, G., Zare, H., Teumer, A., Völker, U., Friedrich, N., Knol, M. J., Satizabal, C. L., Petyuk, V. A., Adams, H. H. H., Launer, L. J., Bennett, D. A., De Jager, P. L., Grabe, H. J., Ikram, M. A., Gudnason, V., Yang, Q., & Seshadri, S. (2020). The genetics of circulating BDNF: towards understanding the role of BDNF in brain structure and function in middle and old ages. Brain communications, 2(2), fcaa176. https://doi.org/10.1093/braincomms/fcaa176
Li, Shuo, et al. "The genetics of circulating BDNF: towards understanding the role of BDNF in brain structure and function in middle and old ages." Brain communications vol. 2,2 (2020): fcaa176. doi: https://doi.org/10.1093/braincomms/fcaa176
Li S, Weinstein G, Zare H, Teumer A, Völker U, Friedrich N, Knol MJ, Satizabal CL, Petyuk VA, Adams HHH, Launer LJ, Bennett DA, De Jager PL, Grabe HJ, Ikram MA, Gudnason V, Yang Q, Seshadri S. The genetics of circulating BDNF: towards understanding the role of BDNF in brain structure and function in middle and old ages. Brain Commun. 2020 Oct 28;2(2):fcaa176. doi: 10.1093/braincomms/fcaa176. eCollection 2020. PMID: 33345186; PMCID: PMC7734441.
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Morphological, Histochemical and Biochemical Features of Cultivated .

Contemporary problems of ecology

Erst AA, Petruk AA, Zibareva LN, Erst AS.
PMID: 34956551
Contemp Probl Ecol. 2021;14(6):701-710. doi: 10.1134/S1995425521060135. Epub 2021 Dec 20.

The study analyzed the content and localization of phenolic compounds, in particular phenylpropanoids, of

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Erst AA, Petruk AA, Zibareva LN, et al. Morphological, Histochemical and Biochemical Features of Cultivated . Contemp Probl Ecol. 2021;14(6):701-710doi: 10.1134/S1995425521060135.
Erst, A. A., Petruk, A. A., Zibareva, L. N., & Erst, A. S. (2021). Morphological, Histochemical and Biochemical Features of Cultivated . Contemporary problems of ecology, 14(6), 701-710. https://doi.org/10.1134/S1995425521060135
Erst, A A, et al. "Morphological, Histochemical and Biochemical Features of Cultivated ." Contemporary problems of ecology vol. 14,6 (2021): 701-710. doi: https://doi.org/10.1134/S1995425521060135
Erst AA, Petruk AA, Zibareva LN, Erst AS. Morphological, Histochemical and Biochemical Features of Cultivated . Contemp Probl Ecol. 2021;14(6):701-710. doi: 10.1134/S1995425521060135. Epub 2021 Dec 20. PMID: 34956551; PMCID: PMC8685791.
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A plastic feedthrough suitable for high-voltage DC femtosecond electron diffractometers.

The Review of scientific instruments

Gicala P, Petruk AA, Rivas N, Netzke S, Pichugin K, Sciaini G.
PMID: 34717399
Rev Sci Instrum. 2021 Oct 01;92(10):103303. doi: 10.1063/5.0058939.

Highly energetic ultrashort electron bunches have the potential to reveal the ultrafast structural dynamics in relatively thicker in-liquid samples. However, direct current voltages higher than 100 kV are exponentially difficult to attain as surface and vacuum breakdown become an...

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Gicala P, Petruk AA, Rivas N, et al. A plastic feedthrough suitable for high-voltage DC femtosecond electron diffractometers. Rev Sci Instrum. 2021;92(10):103303doi: 10.1063/5.0058939.
Gicala, P., Petruk, A. A., Rivas, N., Netzke, S., Pichugin, K., & Sciaini, G. (2021). A plastic feedthrough suitable for high-voltage DC femtosecond electron diffractometers. The Review of scientific instruments, 92(10), 103303. https://doi.org/10.1063/5.0058939
Gicala, Patrick, et al. "A plastic feedthrough suitable for high-voltage DC femtosecond electron diffractometers." The Review of scientific instruments vol. 92,10 (2021): 103303. doi: https://doi.org/10.1063/5.0058939
Gicala P, Petruk AA, Rivas N, Netzke S, Pichugin K, Sciaini G. A plastic feedthrough suitable for high-voltage DC femtosecond electron diffractometers. Rev Sci Instrum. 2021 Oct 01;92(10):103303. doi: 10.1063/5.0058939. PMID: 34717399.
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Deep-Learning-Derived Evaluation Metrics Enable Effective Benchmarking of Computational Tools for Phosphopeptide Identification.

Molecular & cellular proteomics : MCP

Jiang W, Wen B, Li K, Zeng WF, da Veiga Leprevost F, Moon J, Petyuk VA, Edwards NJ, Liu T, Nesvizhskii AI, Zhang B.
PMID: 34737085
Mol Cell Proteomics. 2021 Nov 01;20:100171. doi: 10.1016/j.mcpro.2021.100171. Epub 2021 Nov 01.

Tandem mass spectrometry (MS/MS)-based phosphoproteomics is a powerful technology for global phosphorylation analysis. However, applying four computational pipelines to a typical mass spectrometry (MS)-based phosphoproteomic dataset from a human cancer study, we observed a large discrepancy among the reported...

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Jiang W, Wen B, Li K, et al. Deep-Learning-Derived Evaluation Metrics Enable Effective Benchmarking of Computational Tools for Phosphopeptide Identification. Mol Cell Proteomics. 2021;20:100171doi: 10.1016/j.mcpro.2021.100171.
Jiang, W., Wen, B., Li, K., Zeng, W. F., da Veiga Leprevost, F., Moon, J., Petyuk, V. A., Edwards, N. J., Liu, T., Nesvizhskii, A. I., & Zhang, B. (2021). Deep-Learning-Derived Evaluation Metrics Enable Effective Benchmarking of Computational Tools for Phosphopeptide Identification. Molecular & cellular proteomics : MCP, 20100171. https://doi.org/10.1016/j.mcpro.2021.100171
Jiang, Wen, et al. "Deep-Learning-Derived Evaluation Metrics Enable Effective Benchmarking of Computational Tools for Phosphopeptide Identification." Molecular & cellular proteomics : MCP vol. 20 (2021): 100171. doi: https://doi.org/10.1016/j.mcpro.2021.100171
Jiang W, Wen B, Li K, Zeng WF, da Veiga Leprevost F, Moon J, Petyuk VA, Edwards NJ, Liu T, Nesvizhskii AI, Zhang B. Deep-Learning-Derived Evaluation Metrics Enable Effective Benchmarking of Computational Tools for Phosphopeptide Identification. Mol Cell Proteomics. 2021 Nov 01;20:100171. doi: 10.1016/j.mcpro.2021.100171. Epub 2021 Nov 01. PMID: 34737085; PMCID: PMC8609164.
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Shaped cathodes for the production of ultra-short multi-electron pulses.

Structural dynamics (Melville, N.Y.)

Petruk AA, Pichugin K, Sciaini G.
PMID: 28191483
Struct Dyn. 2017 Jan 25;4(4):044005. doi: 10.1063/1.4974779. eCollection 2017 Jul.

An electrostatic electron source design capable of producing sub-20 femtoseconds (rms) multi-electron pulses is presented. The photoelectron gun concept builds upon geometrical electric field enhancement at the cathode surface. Particle tracer simulations indicate the generation of extremely short bunches...

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Petruk AA, Pichugin K, Sciaini G. Shaped cathodes for the production of ultra-short multi-electron pulses. Struct Dyn. 2017;4(4):044005doi: 10.1063/1.4974779.
Petruk, A. A., Pichugin, K., & Sciaini, G. (2017). Shaped cathodes for the production of ultra-short multi-electron pulses. Structural dynamics (Melville, N.Y.), 4(4), 044005. https://doi.org/10.1063/1.4974779
Petruk, Ariel Alcides, et al. "Shaped cathodes for the production of ultra-short multi-electron pulses." Structural dynamics (Melville, N.Y.) vol. 4,4 (2017): 044005. doi: https://doi.org/10.1063/1.4974779
Petruk AA, Pichugin K, Sciaini G. Shaped cathodes for the production of ultra-short multi-electron pulses. Struct Dyn. 2017 Jan 25;4(4):044005. doi: 10.1063/1.4974779. eCollection 2017 Jul. PMID: 28191483; PMCID: PMC5272824.
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The genetics of circulating BDNF: towards understanding the role of BDNF in brain structure and function in middle and old ages.

Brain communications

Li S, Weinstein G, Zare H, Teumer A, Völker U, Friedrich N, Knol MJ, Satizabal CL, Petyuk VA, Adams HHH, Launer LJ, Bennett DA, De Jager PL, Grabe HJ, Ikram MA, Gudnason V, Yang Q, Seshadri S.
PMID: 33345186
Brain Commun. 2020 Oct 28;2(2):fcaa176. doi: 10.1093/braincomms/fcaa176. eCollection 2020.

Brain-derived neurotrophic factor (BDNF) plays an important role in brain development and function. Substantial amounts of BDNF are present in peripheral blood, and may serve as biomarkers for Alzheimer's disease incidence as well as targets for intervention to reduce...

Cite
Li S, Weinstein G, Zare H, et al. The genetics of circulating BDNF: towards understanding the role of BDNF in brain structure and function in middle and old ages. Brain Commun. 2020;2(2):fcaa176doi: 10.1093/braincomms/fcaa176.
Li, S., Weinstein, G., Zare, H., Teumer, A., Völker, U., Friedrich, N., Knol, M. J., Satizabal, C. L., Petyuk, V. A., Adams, H. H. H., Launer, L. J., Bennett, D. A., De Jager, P. L., Grabe, H. J., Ikram, M. A., Gudnason, V., Yang, Q., & Seshadri, S. (2020). The genetics of circulating BDNF: towards understanding the role of BDNF in brain structure and function in middle and old ages. Brain communications, 2(2), fcaa176. https://doi.org/10.1093/braincomms/fcaa176
Li, Shuo, et al. "The genetics of circulating BDNF: towards understanding the role of BDNF in brain structure and function in middle and old ages." Brain communications vol. 2,2 (2020): fcaa176. doi: https://doi.org/10.1093/braincomms/fcaa176
Li S, Weinstein G, Zare H, Teumer A, Völker U, Friedrich N, Knol MJ, Satizabal CL, Petyuk VA, Adams HHH, Launer LJ, Bennett DA, De Jager PL, Grabe HJ, Ikram MA, Gudnason V, Yang Q, Seshadri S. The genetics of circulating BDNF: towards understanding the role of BDNF in brain structure and function in middle and old ages. Brain Commun. 2020 Oct 28;2(2):fcaa176. doi: 10.1093/braincomms/fcaa176. eCollection 2020. PMID: 33345186; PMCID: PMC7734441.
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Author Correction: Informed-Proteomics: open-source software package for top-down proteomics.

Nature methods

Park J, Piehowski PD, Wilkins C, Zhou M, Mendoza J, Fujimoto GM, Gibbons BC, Shaw JB, Shen Y, Shukla AK, Moore RJ, Liu T, Petyuk VA, Tolić N, Paša-Tolić L, Smith RD, Payne SH, Kim S.
PMID: 29899368
Nat Methods. 2018 Jul;15(7):554. doi: 10.1038/s41592-018-0040-0.

In the version of this article initially published, the authors erroneously reported the search mode that was used for ProSightPC 3.0 in the Online Methods and in Supplementary Table 3.

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Park J, Piehowski PD, Wilkins C, et al. Author Correction: Informed-Proteomics: open-source software package for top-down proteomics. Nat Methods. 2018;15(7):554doi: 10.1038/s41592-018-0040-0.
Park, J., Piehowski, P. D., Wilkins, C., Zhou, M., Mendoza, J., Fujimoto, G. M., Gibbons, B. C., Shaw, J. B., Shen, Y., Shukla, A. K., Moore, R. J., Liu, T., Petyuk, V. A., Tolić, N., Paša-Tolić, L., Smith, R. D., Payne, S. H., & Kim, S. (2018). Author Correction: Informed-Proteomics: open-source software package for top-down proteomics. Nature methods, 15(7), 554. https://doi.org/10.1038/s41592-018-0040-0
Park, Jungkap, et al. "Author Correction: Informed-Proteomics: open-source software package for top-down proteomics." Nature methods vol. 15,7 (2018): 554. doi: https://doi.org/10.1038/s41592-018-0040-0
Park J, Piehowski PD, Wilkins C, Zhou M, Mendoza J, Fujimoto GM, Gibbons BC, Shaw JB, Shen Y, Shukla AK, Moore RJ, Liu T, Petyuk VA, Tolić N, Paša-Tolić L, Smith RD, Payne SH, Kim S. Author Correction: Informed-Proteomics: open-source software package for top-down proteomics. Nat Methods. 2018 Jul;15(7):554. doi: 10.1038/s41592-018-0040-0. PMID: 29899368.
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Correction: Proteogenomic Characterization of Ovarian HGSC Implicates Mitotic Kinases, Replication Stress in Observed Chromosomal Instability.

Cell reports. Medicine

McDermott JE, Arshad OA, Petyuk VA, Fu Y, Gritsenko MA, Clauss TR, Moore RJ, Schepmoes AA, Zhao R, Monroe ME, Schnaubelt M, Tsai CF, Payne SH, Huang C, Wang LB, Foltz S, Wyczalkowski M, Wu Y, Song E, Brewer MA, Thiagarajan M, Kinsinger CR, Robles AI, Boja ES, Rodriguez H, Chan DW, Zhang B, Zhang Z, Ding L, Smith RD, Liu T, Rodland KD.
PMID: 32954372
Cell Rep Med. 2020 Aug 25;1(5). doi: 10.1016/j.xcrm.2020.100075.

[This corrects the article PMC7289043.].

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McDermott JE, Arshad OA, Petyuk VA, et al. Correction: Proteogenomic Characterization of Ovarian HGSC Implicates Mitotic Kinases, Replication Stress in Observed Chromosomal Instability. Cell Rep Med. 2020;1(5)doi: 10.1016/j.xcrm.2020.100075.
McDermott, J. E., Arshad, O. A., Petyuk, V. A., Fu, Y., Gritsenko, M. A., Clauss, T. R., Moore, R. J., Schepmoes, A. A., Zhao, R., Monroe, M. E., Schnaubelt, M., Tsai, C. F., Payne, S. H., Huang, C., Wang, L. B., Foltz, S., Wyczalkowski, M., Wu, Y., Song, E., Brewer, M. A., Thiagarajan, M., Kinsinger, C. R., Robles, A. I., Boja, E. S., Rodriguez, H., Chan, D. W., Zhang, B., Zhang, Z., Ding, L., Smith, R. D., Liu, T., Rodland, K. D. (2020). Correction: Proteogenomic Characterization of Ovarian HGSC Implicates Mitotic Kinases, Replication Stress in Observed Chromosomal Instability. Cell reports. Medicine, 1(5), . https://doi.org/10.1016/j.xcrm.2020.100075
McDermott, Jason E, et al. "Correction: Proteogenomic Characterization of Ovarian HGSC Implicates Mitotic Kinases, Replication Stress in Observed Chromosomal Instability." Cell reports. Medicine vol. 1,5 (2020). doi: https://doi.org/10.1016/j.xcrm.2020.100075
McDermott JE, Arshad OA, Petyuk VA, Fu Y, Gritsenko MA, Clauss TR, Moore RJ, Schepmoes AA, Zhao R, Monroe ME, Schnaubelt M, Tsai CF, Payne SH, Huang C, Wang LB, Foltz S, Wyczalkowski M, Wu Y, Song E, Brewer MA, Thiagarajan M, Kinsinger CR, Robles AI, Boja ES, Rodriguez H, Chan DW, Zhang B, Zhang Z, Ding L, Smith RD, Liu T, Rodland KD. Correction: Proteogenomic Characterization of Ovarian HGSC Implicates Mitotic Kinases, Replication Stress in Observed Chromosomal Instability. Cell Rep Med. 2020 Aug 25;1(5). doi: 10.1016/j.xcrm.2020.100075. PMID: 32954372; PMCID: PMC7500561.
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Synaptic proteins associated with cognitive performance and neuropathology in older humans revealed by multiplexed fractionated proteomics.

Neurobiology of aging

Carlyle BC, Kandigian SE, Kreuzer J, Das S, Trombetta BA, Kuo Y, Bennett DA, Schneider JA, Petyuk VA, Kitchen RR, Morris R, Nairn AC, Hyman BT, Haas W, Arnold SE.
PMID: 34052751
Neurobiol Aging. 2021 Sep;105:99-114. doi: 10.1016/j.neurobiolaging.2021.04.012. Epub 2021 Apr 24.

Alzheimer's disease (AD) is defined by the presence of abundant amyloid-β (Aβ) and tau neuropathology. While this neuropathology is necessary for AD diagnosis, it is not sufficient for causing cognitive impairment. Up to one third of community dwelling older...

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Carlyle BC, Kandigian SE, Kreuzer J, et al. Synaptic proteins associated with cognitive performance and neuropathology in older humans revealed by multiplexed fractionated proteomics. Neurobiol Aging. 2021;105:99-114doi: 10.1016/j.neurobiolaging.2021.04.012.
Carlyle, B. C., Kandigian, S. E., Kreuzer, J., Das, S., Trombetta, B. A., Kuo, Y., Bennett, D. A., Schneider, J. A., Petyuk, V. A., Kitchen, R. R., Morris, R., Nairn, A. C., Hyman, B. T., Haas, W., & Arnold, S. E. (2021). Synaptic proteins associated with cognitive performance and neuropathology in older humans revealed by multiplexed fractionated proteomics. Neurobiology of aging, 10599-114. https://doi.org/10.1016/j.neurobiolaging.2021.04.012
Carlyle, Becky C, et al. "Synaptic proteins associated with cognitive performance and neuropathology in older humans revealed by multiplexed fractionated proteomics." Neurobiology of aging vol. 105 (2021): 99-114. doi: https://doi.org/10.1016/j.neurobiolaging.2021.04.012
Carlyle BC, Kandigian SE, Kreuzer J, Das S, Trombetta BA, Kuo Y, Bennett DA, Schneider JA, Petyuk VA, Kitchen RR, Morris R, Nairn AC, Hyman BT, Haas W, Arnold SE. Synaptic proteins associated with cognitive performance and neuropathology in older humans revealed by multiplexed fractionated proteomics. Neurobiol Aging. 2021 Sep;105:99-114. doi: 10.1016/j.neurobiolaging.2021.04.012. Epub 2021 Apr 24. PMID: 34052751; PMCID: PMC8338777.
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