(g) Pathway Mapping—The Mapp to KEGG pathways node
maps compounds to biological pathways using KEGG.
The Map to Metabolika Pathways node maps compounds
to biological pathways using Metabolika.
(h) Compound Scoring—The Apply mzLogic node applies
mzLogic algorithm to rank order ChemSpider results.
(i) Expected Compounds—No nodes were selected.
(j) Post-processing. The Differential Analysis node calculates
differential analysis (t-test or ANOVA). The Descriptive
Statistics node determines p-values, adjusted p-values,
ratios, fold change, CV, etc.
Acknowledgments
We thank Mr. John Orlando from Thermo Scientific Inc. for assistance with Acquire X on the Orbitrap Fusion Tribrid LC-MS
n
system. The work is partly supported by a grant from the National
Science Foundation (MCB 1758820) to S. Chen.
References
1. Afendi FM, Okada T, Yamazaki M, HiraiMorita A, Nakamura Y, Nakamura K, Ikeda S,
Takahashi H, Altaf-Ul Amin M, Darusman LK,
Saito K, Kanaya S (2012) KNApSAcK family
databases: Integrated metabolite-plant species
databases for multifaceted plant research. Plant
Cell Physiol 53(2):e1–e12. https://doi.org/
10.1093/pcp/pcr165
2. Sumner LW, Amberg A, Barrett D, Beale M,
Beger R, Daykin CA, Fan TW-M, Fiehn O,
Goodacre R, Griffin JL, Hankemeier T,
Hardy N, Harnly J (2007) Proposed minimum
reporting standards for chemical analysis.
Chemical analysis working group (CAWG).
Metabolomics standards initiative (MSI).
Metabolomics 3(3):211–221. https://doi.
org/10.1007/s11306-007-0082-2
3. Yang X, Wei S, Liu B, Guo D, Zheng B,
Feng L, Liu Y, Toma ´s-Barbera ´n FA, Luo L,
Huang D (2018) A novel integrated
non-targeted metabolomic analysis reveals significant metabolite variations between different
lettuce (Lactuca sativa L.) varieties. Horticult
Res 5(33):1–14. https://doi.org/10.1038/
s41438-018-0050-1
4. Caman ˜es G, Scalschi L, Vicedo B, Gonza ´lezBosch C, Garcı ´a-Agustı ´n P (2015) An untargeted global metabolomic analysis reveals the
biochemical changes underlying basal resistance and priming in Solanum lycopersicum,
and identifies 1-methyltryptophan as a metabolite involved in plant responses to Botrytis
cinerea and Pseudomonas syringae. Plant J 84
(1):125–139. https://doi.org/10.1111/tpj.
12964
5. Misra BB, Acharya BR, Granot D, Assmann
SM, Chen S (2015) The guard cell metabolome: functions in stomatal movement and
global food security. Front Plant Sci 6
(334):1–13. https://doi.org/10.3389/fpls.
2015.00334
6. Misra BB, Assmann SM, Chen S (2014) Plant
single cell and single cell-type metabolomics.
Trends Plant Sci 19:637–646
7. Zhu M, Jeon BW, Geng S, Yu Y, Balmant K,
Chen S, Assmann S (2016) Preparation of epidermal peels and guard cell protoplasts for cellular, electrophysiological, and -omics assays of
guard cell function. In: Botella J, Botella M
(eds) Plant signal transduction, Methods in
molecular biology, vol 1363. Humana Press,
New York. https://doi.org/10.1007/978-14939-3115-6_9
8. David L, Harmon AC, Chen S (2019) Plant
immune responses - from guard cells and local
responses to systemic defense against bacterial
pathogens. Plant Signal Behav 14(5):1–9.
https://doi.org/10.1080/15592324.2019.
1588667
Untargeted Metabolomics of Arabidopsis Stomatal Immunity
423
maps compounds to biological pathways using KEGG.
The Map to Metabolika Pathways node maps compounds
to biological pathways using Metabolika.
(h) Compound Scoring—The Apply mzLogic node applies
mzLogic algorithm to rank order ChemSpider results.
(i) Expected Compounds—No nodes were selected.
(j) Post-processing. The Differential Analysis node calculates
differential analysis (t-test or ANOVA). The Descriptive
Statistics node determines p-values, adjusted p-values,
ratios, fold change, CV, etc.
Acknowledgments
We thank Mr. John Orlando from Thermo Scientific Inc. for assistance with Acquire X on the Orbitrap Fusion Tribrid LC-MS
n
system. The work is partly supported by a grant from the National
Science Foundation (MCB 1758820) to S. Chen.
References
1. Afendi FM, Okada T, Yamazaki M, HiraiMorita A, Nakamura Y, Nakamura K, Ikeda S,
Takahashi H, Altaf-Ul Amin M, Darusman LK,
Saito K, Kanaya S (2012) KNApSAcK family
databases: Integrated metabolite-plant species
databases for multifaceted plant research. Plant
Cell Physiol 53(2):e1–e12. https://doi.org/
10.1093/pcp/pcr165
2. Sumner LW, Amberg A, Barrett D, Beale M,
Beger R, Daykin CA, Fan TW-M, Fiehn O,
Goodacre R, Griffin JL, Hankemeier T,
Hardy N, Harnly J (2007) Proposed minimum
reporting standards for chemical analysis.
Chemical analysis working group (CAWG).
Metabolomics standards initiative (MSI).
Metabolomics 3(3):211–221. https://doi.
org/10.1007/s11306-007-0082-2
3. Yang X, Wei S, Liu B, Guo D, Zheng B,
Feng L, Liu Y, Toma ´s-Barbera ´n FA, Luo L,
Huang D (2018) A novel integrated
non-targeted metabolomic analysis reveals significant metabolite variations between different
lettuce (Lactuca sativa L.) varieties. Horticult
Res 5(33):1–14. https://doi.org/10.1038/
s41438-018-0050-1
4. Caman ˜es G, Scalschi L, Vicedo B, Gonza ´lezBosch C, Garcı ´a-Agustı ´n P (2015) An untargeted global metabolomic analysis reveals the
biochemical changes underlying basal resistance and priming in Solanum lycopersicum,
and identifies 1-methyltryptophan as a metabolite involved in plant responses to Botrytis
cinerea and Pseudomonas syringae. Plant J 84
(1):125–139. https://doi.org/10.1111/tpj.
12964
5. Misra BB, Acharya BR, Granot D, Assmann
SM, Chen S (2015) The guard cell metabolome: functions in stomatal movement and
global food security. Front Plant Sci 6
(334):1–13. https://doi.org/10.3389/fpls.
2015.00334
6. Misra BB, Assmann SM, Chen S (2014) Plant
single cell and single cell-type metabolomics.
Trends Plant Sci 19:637–646
7. Zhu M, Jeon BW, Geng S, Yu Y, Balmant K,
Chen S, Assmann S (2016) Preparation of epidermal peels and guard cell protoplasts for cellular, electrophysiological, and -omics assays of
guard cell function. In: Botella J, Botella M
(eds) Plant signal transduction, Methods in
molecular biology, vol 1363. Humana Press,
New York. https://doi.org/10.1007/978-14939-3115-6_9
8. David L, Harmon AC, Chen S (2019) Plant
immune responses - from guard cells and local
responses to systemic defense against bacterial
pathogens. Plant Signal Behav 14(5):1–9.
https://doi.org/10.1080/15592324.2019.
1588667
Untargeted Metabolomics of Arabidopsis Stomatal Immunity
423