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Soybean Roots Grown under Heat Stress Show Global Changes in Their Transcriptional and Proteomic Profiles.

Frontiers in plant science

Valdés-López O, Batek J, Gomez-Hernandez N, Nguyen CT, Isidra-Arellano MC, Zhang N, Joshi T, Xu D, Hixson KK, Weitz KK, Aldrich JT, Paša-Tolić L, Stacey G.
PMID: 27200004
Front Plant Sci. 2016 Apr 25;7:517. doi: 10.3389/fpls.2016.00517. eCollection 2016.

Heat stress is likely to be a key factor in the negative impact of climate change on crop production. Heat stress significantly influences the functions of roots, which provide support, water, and nutrients to other plant organs. Likewise, roots...

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Valdés-López O, Batek J, Gomez-Hernandez N, et al. Soybean Roots Grown under Heat Stress Show Global Changes in Their Transcriptional and Proteomic Profiles. Front Plant Sci. 2016;7:517doi: 10.3389/fpls.2016.00517.
Valdés-López, O., Batek, J., Gomez-Hernandez, N., Nguyen, C. T., Isidra-Arellano, M. C., Zhang, N., Joshi, T., Xu, D., Hixson, K. K., Weitz, K. K., Aldrich, J. T., Paša-Tolić, L., & Stacey, G. (2016). Soybean Roots Grown under Heat Stress Show Global Changes in Their Transcriptional and Proteomic Profiles. Frontiers in plant science, 7517. https://doi.org/10.3389/fpls.2016.00517
Valdés-López, Oswaldo, et al. "Soybean Roots Grown under Heat Stress Show Global Changes in Their Transcriptional and Proteomic Profiles." Frontiers in plant science vol. 7 (2016): 517. doi: https://doi.org/10.3389/fpls.2016.00517
Valdés-López O, Batek J, Gomez-Hernandez N, Nguyen CT, Isidra-Arellano MC, Zhang N, Joshi T, Xu D, Hixson KK, Weitz KK, Aldrich JT, Paša-Tolić L, Stacey G. Soybean Roots Grown under Heat Stress Show Global Changes in Their Transcriptional and Proteomic Profiles. Front Plant Sci. 2016 Apr 25;7:517. doi: 10.3389/fpls.2016.00517. eCollection 2016. PMID: 27200004; PMCID: PMC4843095.
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ESI-FTICR mass spectrometry employing data-dependent external ion selection and accumulation.

Journal of the American Society for Mass Spectrometry

Harkewicz R, Belov ME, Anderson GA, Pasa-Tolić L, Masselon CD, Prior DC, Udseth HR, Smith RD.
PMID: 11838018
J Am Soc Mass Spectrom. 2002 Feb;13(2):144-54. doi: 10.1016/S1044-0305(01)00343-9.

Data-dependent external m/z selection and accumulation of ions is demonstrated in use with ESI-FTICR instrumentation, with two different methods for ion selection being explored. One method uses RF/DC quadrupole filtering and is described in use with an 11.5 tesla...

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Harkewicz R, Belov ME, Anderson GA, et al. ESI-FTICR mass spectrometry employing data-dependent external ion selection and accumulation. J Am Soc Mass Spectrom. 2002;13(2):144-54doi: 10.1016/S1044-0305(01)00343-9.
Harkewicz, R., Belov, M. E., Anderson, G. A., Pasa-Tolić, L., Masselon, C. D., Prior, D. C., Udseth, H. R., & Smith, R. D. (2002). ESI-FTICR mass spectrometry employing data-dependent external ion selection and accumulation. Journal of the American Society for Mass Spectrometry, 13(2), 144-54. https://doi.org/10.1016/S1044-0305(01)00343-9
Harkewicz, Richard, et al. "ESI-FTICR mass spectrometry employing data-dependent external ion selection and accumulation." Journal of the American Society for Mass Spectrometry vol. 13,2 (2002): 144-54. doi: https://doi.org/10.1016/S1044-0305(01)00343-9
Harkewicz R, Belov ME, Anderson GA, Pasa-Tolić L, Masselon CD, Prior DC, Udseth HR, Smith RD. ESI-FTICR mass spectrometry employing data-dependent external ion selection and accumulation. J Am Soc Mass Spectrom. 2002 Feb;13(2):144-54. doi: 10.1016/S1044-0305(01)00343-9. PMID: 11838018.
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High resolution techniques: general discussion.

Faraday discussions

Adair E, Afonso C, Bell NGA, Davies AN, Delsuc MA, Godfrey R, Goodacre R, Hawkes JA, Hertkorn N, Jones D, Lameiras P, Le Guennec A, Lubben A, Nilsson M, Paša-Tolić L, Richards J, Rodgers RP, Rüger CP, Schmitt-Kopplin P, Schoenmakers PJ, Sidebottom P, Staerk D, Summerfield S, Uhrín D, van Delft P, van der Hooft JJJ, van Zelst FHM, Zherebker A.
PMID: 31369012
Faraday Discuss. 2019 Aug 15;218:247-267. doi: 10.1039/c9fd90045d.

No abstract available.

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Adair E, Afonso C, Bell NGA, et al. High resolution techniques: general discussion. Faraday Discuss. 2019;218:247-267doi: 10.1039/c9fd90045d.
Adair, E., Afonso, C., Bell, N. G. A., Davies, A. N., Delsuc, M. A., Godfrey, R., Goodacre, R., Hawkes, J. A., Hertkorn, N., Jones, D., Lameiras, P., Le Guennec, A., Lubben, A., Nilsson, M., Paša-Tolić, L., Richards, J., Rodgers, R. P., Rüger, C. P., Schmitt-Kopplin, P., Schoenmakers, P. J., Sidebottom, P., Staerk, D., Summerfield, S., Uhrín, D., van Delft, P., van der Hooft, J. J. J., van Zelst, F. H. M., & Zherebker, A. (2019). High resolution techniques: general discussion. Faraday discussions, 218247-267. https://doi.org/10.1039/c9fd90045d
Adair, Elaine, et al. "High resolution techniques: general discussion." Faraday discussions vol. 218 (2019): 247-267. doi: https://doi.org/10.1039/c9fd90045d
Adair E, Afonso C, Bell NGA, Davies AN, Delsuc MA, Godfrey R, Goodacre R, Hawkes JA, Hertkorn N, Jones D, Lameiras P, Le Guennec A, Lubben A, Nilsson M, Paša-Tolić L, Richards J, Rodgers RP, Rüger CP, Schmitt-Kopplin P, Schoenmakers PJ, Sidebottom P, Staerk D, Summerfield S, Uhrín D, van Delft P, van der Hooft JJJ, van Zelst FHM, Zherebker A. High resolution techniques: general discussion. Faraday Discuss. 2019 Aug 15;218:247-267. doi: 10.1039/c9fd90045d. PMID: 31369012.
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Formularity: Software for Automated Formula Assignment of Natural and Other Organic Matter from Ultrahigh-Resolution Mass Spectra.

Analytical chemistry

Tolić N, Liu Y, Liyu A, Shen Y, Tfaily MM, Kujawinski EB, Longnecker K, Kuo LJ, Robinson EW, Paša-Tolić L, Hess NJ.
PMID: 29120613
Anal Chem. 2017 Dec 05;89(23):12659-12665. doi: 10.1021/acs.analchem.7b03318. Epub 2017 Nov 21.

Ultrahigh resolution mass spectrometry, such as Fourier transform ion cyclotron resonance mass spectrometry (FT ICR MS), can resolve thousands of molecular ions in complex organic matrices. A Compound Identification Algorithm (CIA) was previously developed for automated elemental formula assignment...

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Tolić N, Liu Y, Liyu A, et al. Formularity: Software for Automated Formula Assignment of Natural and Other Organic Matter from Ultrahigh-Resolution Mass Spectra. Anal Chem. 2017;89(23):12659-12665doi: 10.1021/acs.analchem.7b03318.
Tolić, N., Liu, Y., Liyu, A., Shen, Y., Tfaily, M. M., Kujawinski, E. B., Longnecker, K., Kuo, L. J., Robinson, E. W., Paša-Tolić, L., & Hess, N. J. (2017). Formularity: Software for Automated Formula Assignment of Natural and Other Organic Matter from Ultrahigh-Resolution Mass Spectra. Analytical chemistry, 89(23), 12659-12665. https://doi.org/10.1021/acs.analchem.7b03318
Tolić, Nikola, et al. "Formularity: Software for Automated Formula Assignment of Natural and Other Organic Matter from Ultrahigh-Resolution Mass Spectra." Analytical chemistry vol. 89,23 (2017): 12659-12665. doi: https://doi.org/10.1021/acs.analchem.7b03318
Tolić N, Liu Y, Liyu A, Shen Y, Tfaily MM, Kujawinski EB, Longnecker K, Kuo LJ, Robinson EW, Paša-Tolić L, Hess NJ. Formularity: Software for Automated Formula Assignment of Natural and Other Organic Matter from Ultrahigh-Resolution Mass Spectra. Anal Chem. 2017 Dec 05;89(23):12659-12665. doi: 10.1021/acs.analchem.7b03318. Epub 2017 Nov 21. PMID: 29120613.
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Metabolic Interactions between .

mSystems

Boiteau RM, Markillie LM, Hoyt DW, Hu D, Chu RK, Mitchell HD, Pasa-Tolic L, Jansson JK, Jansson C.
PMID: 33402348
mSystems. 2021 Jan 05;6(1). doi: 10.1128/mSystems.00580-20.

Iron (Fe) availability has well-known effects on plant and microbial metabolism, but its effects on interspecies interactions are poorly understood. The purpose of this study was to investigate metabolite exchange between the grass

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Boiteau RM, Markillie LM, Hoyt DW, et al. Metabolic Interactions between . mSystems. 2021;6(1)doi: 10.1128/mSystems.00580-20.
Boiteau, R. M., Markillie, L. M., Hoyt, D. W., Hu, D., Chu, R. K., Mitchell, H. D., Pasa-Tolic, L., Jansson, J. K., & Jansson, C. (2021). Metabolic Interactions between . mSystems, 6(1), . https://doi.org/10.1128/mSystems.00580-20
Boiteau, Rene M, et al. "Metabolic Interactions between ." mSystems vol. 6,1 (2021). doi: https://doi.org/10.1128/mSystems.00580-20
Boiteau RM, Markillie LM, Hoyt DW, Hu D, Chu RK, Mitchell HD, Pasa-Tolic L, Jansson JK, Jansson C. Metabolic Interactions between . mSystems. 2021 Jan 05;6(1). doi: 10.1128/mSystems.00580-20. PMID: 33402348; PMCID: PMC7786132.
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Metabolic Noise and Distinct Subpopulations Observed by Single Cell LAESI Mass Spectrometry of Plant Cells .

Frontiers in plant science

Stopka SA, Khattar R, Agtuca BJ, Anderton CR, Paša-Tolić L, Stacey G, Vertes A.
PMID: 30498504
Front Plant Sci. 2018 Nov 15;9:1646. doi: 10.3389/fpls.2018.01646. eCollection 2018.

Phenotypic variations and stochastic expression of transcripts, proteins, and metabolites in biological tissues lead to cellular heterogeneity. As a result, distinct cellular subpopulations emerge. They are characterized by different metabolite expression levels and by associated metabolic noise distributions. To...

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Stopka SA, Khattar R, Agtuca BJ, et al. Metabolic Noise and Distinct Subpopulations Observed by Single Cell LAESI Mass Spectrometry of Plant Cells . Front Plant Sci. 2018;9:1646doi: 10.3389/fpls.2018.01646.
Stopka, S. A., Khattar, R., Agtuca, B. J., Anderton, C. R., Paša-Tolić, L., Stacey, G., & Vertes, A. (2018). Metabolic Noise and Distinct Subpopulations Observed by Single Cell LAESI Mass Spectrometry of Plant Cells . Frontiers in plant science, 91646. https://doi.org/10.3389/fpls.2018.01646
Stopka, Sylwia A, et al. "Metabolic Noise and Distinct Subpopulations Observed by Single Cell LAESI Mass Spectrometry of Plant Cells ." Frontiers in plant science vol. 9 (2018): 1646. doi: https://doi.org/10.3389/fpls.2018.01646
Stopka SA, Khattar R, Agtuca BJ, Anderton CR, Paša-Tolić L, Stacey G, Vertes A. Metabolic Noise and Distinct Subpopulations Observed by Single Cell LAESI Mass Spectrometry of Plant Cells . Front Plant Sci. 2018 Nov 15;9:1646. doi: 10.3389/fpls.2018.01646. eCollection 2018. PMID: 30498504; PMCID: PMC6250120.
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Data mining and visualisation: general discussion.

Faraday discussions

Afonso C, Barrow MP, Davies AN, Delsuc MA, Ebbels T, Fernandez-Lima F, Gauchotte-Lindsay C, Giusti P, Goodacre R, Hertkorn N, Jansen JJ, Jones D, Kew W, Kuhn S, Le Guennec A, Lubben A, Parkinson J, Paša-Tolić L, Rogers S, Rudd TR, Schoenmakers PJ, Sidebottom P, Summerfield S, Tinnevelt GH, Trifirò G, Trygg J, van der Hooft JJJ.
PMID: 31373341
Faraday Discuss. 2019 Aug 15;218:354-371. doi: 10.1039/C9FD90044F.

No abstract available.

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Afonso C, Barrow MP, Davies AN, et al. Data mining and visualisation: general discussion. Faraday Discuss. 2019;218:354-371doi: 10.1039/C9FD90044F.
Afonso, C., Barrow, M. P., Davies, A. N., Delsuc, M. A., Ebbels, T., Fernandez-Lima, F., Gauchotte-Lindsay, C., Giusti, P., Goodacre, R., Hertkorn, N., Jansen, J. J., Jones, D., Kew, W., Kuhn, S., Le Guennec, A., Lubben, A., Parkinson, J., Paša-Tolić, L., Rogers, S., Rudd, T. R., Schoenmakers, P. J., Sidebottom, P., Summerfield, S., Tinnevelt, G. H., Trifirò, G., Trygg, J., & van der Hooft, J. J. J. (2019). Data mining and visualisation: general discussion. Faraday discussions, 218354-371. https://doi.org/10.1039/C9FD90044F
Afonso, Carlos, et al. "Data mining and visualisation: general discussion." Faraday discussions vol. 218 (2019): 354-371. doi: https://doi.org/10.1039/C9FD90044F
Afonso C, Barrow MP, Davies AN, Delsuc MA, Ebbels T, Fernandez-Lima F, Gauchotte-Lindsay C, Giusti P, Goodacre R, Hertkorn N, Jansen JJ, Jones D, Kew W, Kuhn S, Le Guennec A, Lubben A, Parkinson J, Paša-Tolić L, Rogers S, Rudd TR, Schoenmakers PJ, Sidebottom P, Summerfield S, Tinnevelt GH, Trifirò G, Trygg J, van der Hooft JJJ. Data mining and visualisation: general discussion. Faraday Discuss. 2019 Aug 15;218:354-371. doi: 10.1039/C9FD90044F. PMID: 31373341.
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Close and distant: Contrasting the metabolism of two closely related subspecies of Scots pine under the effects of folivory and summer drought.

Ecology and evolution

Rivas-Ubach A, Sardans J, Hódar JA, Garcia-Porta J, Guenther A, Paša-Tolić L, Oravec M, Urban O, Peñuelas J.
PMID: 29152192
Ecol Evol. 2017 Sep 25;7(21):8976-8988. doi: 10.1002/ece3.3343. eCollection 2017 Nov.

Metabolomes, as chemical phenotypes of organisms, are likely not only shaped by the environment but also by common ancestry. If this is the case, we expect that closely related species of pines will tend to reach similar metabolomic solutions...

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Rivas-Ubach A, Sardans J, Hódar JA, et al. Close and distant: Contrasting the metabolism of two closely related subspecies of Scots pine under the effects of folivory and summer drought. Ecol Evol. 2017;7(21):8976-8988doi: 10.1002/ece3.3343.
Rivas-Ubach, A., Sardans, J., Hódar, J. A., Garcia-Porta, J., Guenther, A., Paša-Tolić, L., Oravec, M., Urban, O., & Peñuelas, J. (2017). Close and distant: Contrasting the metabolism of two closely related subspecies of Scots pine under the effects of folivory and summer drought. Ecology and evolution, 7(21), 8976-8988. https://doi.org/10.1002/ece3.3343
Rivas-Ubach, Albert, et al. "Close and distant: Contrasting the metabolism of two closely related subspecies of Scots pine under the effects of folivory and summer drought." Ecology and evolution vol. 7,21 (2017): 8976-8988. doi: https://doi.org/10.1002/ece3.3343
Rivas-Ubach A, Sardans J, Hódar JA, Garcia-Porta J, Guenther A, Paša-Tolić L, Oravec M, Urban O, Peñuelas J. Close and distant: Contrasting the metabolism of two closely related subspecies of Scots pine under the effects of folivory and summer drought. Ecol Evol. 2017 Sep 25;7(21):8976-8988. doi: 10.1002/ece3.3343. eCollection 2017 Nov. PMID: 29152192; PMCID: PMC5677489.
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Subnanogram proteomics: impact of LC column selection, MS instrumentation and data analysis strategy on proteome coverage for trace samples.

International journal of mass spectrometry

Zhu Y, Zhao R, Piehowski PD, Moore RJ, Lim S, Orphan VJ, Paša-Tolić L, Qian WJ, Smith RD, Kelly RT.
PMID: 29576737
Int J Mass Spectrom. 2018 Apr;427:4-10. doi: 10.1016/j.ijms.2017.08.016. Epub 2017 Sep 01.

One of the greatest challenges for mass spectrometry (MS)-based proteomics is the limited ability to analyze small samples. Here we investigate the relative contributions of liquid chromatography (LC), MS instrumentation and data analysis methods with the aim of improving...

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Zhu Y, Zhao R, Piehowski PD, et al. Subnanogram proteomics: impact of LC column selection, MS instrumentation and data analysis strategy on proteome coverage for trace samples. Int J Mass Spectrom. 2017;427:4-10doi: 10.1016/j.ijms.2017.08.016.
Zhu, Y., Zhao, R., Piehowski, P. D., Moore, R. J., Lim, S., Orphan, V. J., Paša-Tolić, L., Qian, W. J., Smith, R. D., & Kelly, R. T. (2018). Subnanogram proteomics: impact of LC column selection, MS instrumentation and data analysis strategy on proteome coverage for trace samples. International journal of mass spectrometry, 4274-10. https://doi.org/10.1016/j.ijms.2017.08.016
Zhu, Ying, et al. "Subnanogram proteomics: impact of LC column selection, MS instrumentation and data analysis strategy on proteome coverage for trace samples." International journal of mass spectrometry vol. 427 (2018): 4-10. doi: https://doi.org/10.1016/j.ijms.2017.08.016
Zhu Y, Zhao R, Piehowski PD, Moore RJ, Lim S, Orphan VJ, Paša-Tolić L, Qian WJ, Smith RD, Kelly RT. Subnanogram proteomics: impact of LC column selection, MS instrumentation and data analysis strategy on proteome coverage for trace samples. Int J Mass Spectrom. 2018 Apr;427:4-10. doi: 10.1016/j.ijms.2017.08.016. Epub 2017 Sep 01. PMID: 29576737; PMCID: PMC5863755.
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Quantitative Proteomic Profiling of Low-Dose Ionizing Radiation Effects in a Human Skin Model.

Proteomes

Hengel SM, Aldrich JT, Waters KM, Pasa-Tolic L, Stenoien DL.
PMID: 28250387
Proteomes. 2014 Jul 29;2(3):382-398. doi: 10.3390/proteomes2030382.

To assess responses to low-dose ionizing radiation (LD-IR) exposures potentially encountered during medical diagnostic procedures, nuclear accidents or terrorist acts, a quantitative proteomic approach was used to identify changes in protein abundance in a reconstituted human skin tissue model...

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Hengel SM, Aldrich JT, Waters KM, et al. Quantitative Proteomic Profiling of Low-Dose Ionizing Radiation Effects in a Human Skin Model. Proteomes. 2014;2(3):382-398doi: 10.3390/proteomes2030382.
Hengel, S. M., Aldrich, J. T., Waters, K. M., Pasa-Tolic, L., & Stenoien, D. L. (2014). Quantitative Proteomic Profiling of Low-Dose Ionizing Radiation Effects in a Human Skin Model. Proteomes, 2(3), 382-398. https://doi.org/10.3390/proteomes2030382
Hengel, Shawna M, et al. "Quantitative Proteomic Profiling of Low-Dose Ionizing Radiation Effects in a Human Skin Model." Proteomes vol. 2,3 (2014): 382-398. doi: https://doi.org/10.3390/proteomes2030382
Hengel SM, Aldrich JT, Waters KM, Pasa-Tolic L, Stenoien DL. Quantitative Proteomic Profiling of Low-Dose Ionizing Radiation Effects in a Human Skin Model. Proteomes. 2014 Jul 29;2(3):382-398. doi: 10.3390/proteomes2030382. PMID: 28250387; PMCID: PMC5302749.
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Application of printed circuit board technology to FT-ICR MS analyzer cell construction and prototyping.

Journal of the American Society for Mass Spectrometry

Leach FE, Norheim R, Anderson G, Pasa-Tolic L.
PMID: 25056862
J Am Soc Mass Spectrom. 2014 Dec;25(12):2069-72. doi: 10.1007/s13361-014-0952-6. Epub 2014 Jul 24.

Although Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) remains the mass spectrometry platform that provides the highest levels of performance for mass accuracy and resolving power, there is room for improvement in analyzer cell design as the...

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Leach FE, Norheim R, Anderson G, et al. Application of printed circuit board technology to FT-ICR MS analyzer cell construction and prototyping. J Am Soc Mass Spectrom. 2014;25(12):2069-72doi: 10.1007/s13361-014-0952-6.
Leach, F. E., Norheim, R., Anderson, G., & Pasa-Tolic, L. (2014). Application of printed circuit board technology to FT-ICR MS analyzer cell construction and prototyping. Journal of the American Society for Mass Spectrometry, 25(12), 2069-72. https://doi.org/10.1007/s13361-014-0952-6
Leach, Franklin E, et al. "Application of printed circuit board technology to FT-ICR MS analyzer cell construction and prototyping." Journal of the American Society for Mass Spectrometry vol. 25,12 (2014): 2069-72. doi: https://doi.org/10.1007/s13361-014-0952-6
Leach FE, Norheim R, Anderson G, Pasa-Tolic L. Application of printed circuit board technology to FT-ICR MS analyzer cell construction and prototyping. J Am Soc Mass Spectrom. 2014 Dec;25(12):2069-72. doi: 10.1007/s13361-014-0952-6. Epub 2014 Jul 24. PMID: 25056862.
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Interactions between microbial diversity and substrate chemistry determine the fate of carbon in soil.

Scientific reports

Raczka NC, Piñeiro J, Tfaily MM, Chu RK, Lipton MS, Pasa-Tolic L, Morrissey E, Brzostek E.
PMID: 34588474
Sci Rep. 2021 Sep 29;11(1):19320. doi: 10.1038/s41598-021-97942-9.

Microbial decomposition drives the transformation of plant-derived substrates into microbial products that form stable soil organic matter (SOM). Recent theories have posited that decomposition depends on an interaction between SOM chemistry with microbial diversity and resulting function (e.g., enzymatic...

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Raczka NC, Piñeiro J, Tfaily MM, et al. Interactions between microbial diversity and substrate chemistry determine the fate of carbon in soil. Sci Rep. 2021;11(1):19320doi: 10.1038/s41598-021-97942-9.
Raczka, N. C., Piñeiro, J., Tfaily, M. M., Chu, R. K., Lipton, M. S., Pasa-Tolic, L., Morrissey, E., & Brzostek, E. (2021). Interactions between microbial diversity and substrate chemistry determine the fate of carbon in soil. Scientific reports, 11(1), 19320. https://doi.org/10.1038/s41598-021-97942-9
Raczka, Nanette C, et al. "Interactions between microbial diversity and substrate chemistry determine the fate of carbon in soil." Scientific reports vol. 11,1 (2021): 19320. doi: https://doi.org/10.1038/s41598-021-97942-9
Raczka NC, Piñeiro J, Tfaily MM, Chu RK, Lipton MS, Pasa-Tolic L, Morrissey E, Brzostek E. Interactions between microbial diversity and substrate chemistry determine the fate of carbon in soil. Sci Rep. 2021 Sep 29;11(1):19320. doi: 10.1038/s41598-021-97942-9. PMID: 34588474; PMCID: PMC8481224.
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