15. Default settings in MaxQuant are suggested to be left
unchanged; for analysis of modifications, such as phosphorylation, variable modifications need to be defined. In-depth information about MaxQuant settings is described in [22].
References
1. Benschop JJ, Mohammed S, O’Flaherty M,
Heck AJ, Slijper M, Menke FL (2007) Quantitative phospho-proteomics of early elicitor signalling in Arabidopsis. Mol Cell Proteomics 6
(7):1705–1713
2. Chen Y, Ho ¨henwarter W, Weckwerth W
(2010) Comparative analysis of phytohormone—responsive phosphoproteins in Arabidopsis thaliana using TiO 2 -phosphopeptide
enrichment and MAPA. Plant J 63(1):1–17
3. Chinchilla D, Zipfel C, Robatzek S,
Kemmerling B, Nurnberger T, Jones JD,
Felix G, Boller T (2007) A flagellin-induced
complex of the receptor FLS2 and BAK1 initiates
plant
defence.
Nature
448
(7152):497–500. https://doi.org/10.1038/
nature05999
4. Cox J, Mann M (2008) MaxQuant enables
high peptide identification rates, individualized
p.p.b.-range mass accuracies and proteomewide protein quantification. Nat Biotechnol
26(12):1367–1372.
https://doi.org/10.
1038/nbt.1511
5. Engelsberger WR, Schulze WX (2012) Nitrate
and ammonium lead to distinct global dynamic
phosphorylation patterns when resupplied to
nitrogen starved Arabidopsis seedlings. Plant J
69(6):978–995
6. Haruta M, Gray WM, Sussman MR (2015)
Regulation of the plasma membrane proton
pump (H(+)-ATPase) by phosphorylation.
Curr Opin Plant Biol 28:68–75. https://doi.
org/10.1016/j.pbi.2015.09.005
7. Kerk D, Bulgrien J, Smith DW, Barsam B,
Veretnik S, Gribskov M (2002) The complement of protein phosphatase catalytic subunits
encoded in the genome of Arabidopsis. Plant
Physiol 129(2):908–925. https://doi.org/10.
1104/pp.004002
8. Kim TW, Guan S, Sun Y, Deng Z, Tang W,
Shang JX, Sun Y, Burlingam A, Wang ZY
(2009) Brassinosteroid signal transduction
from cell-surface receptor kinases to nuclear
transcription factors. Nat Cell Biol 11
(10):1254–1260
9. Lan P, Li W, Wen TN, Schmidt W (2012)
Quantitative phosphoproteome profiling of
iron-deficient Arabidopsis roots. Plant Physiol
159(1):403–417
10. Marshall A, Aalen RB, Audenaert D,
Beeckman T, Broadley MR, Butenko MA,
Can ˜o-Delgado AI et al (2012) Tackling
drought stress: receptor-like kinases present
new approaches. Plant Cell 24(6):2262–2278
11. Menz J, Li Z, Schulze WX, Ludewig U (2016)
Early nitrogen-deprivation responses in Arabidopsis roots reveal distinct differences on transcriptome and (phospho-) proteome levels
between nitrate and ammonium nutrition.
Plant J 88(5):717–734. https://doi.org/10.
1111/tpj.13272
12. Niittyl€ a T, Fuglsang AT, Palmgren MG, Frommer WB, Schulze WX (2007) Temporal analysis of sucrose-induced phosphorylation
changes in plasma membrane proteins of Arabidopsis.
Mol
Cell
Proteomics
6
(10):1711–1726
13. Osakabe
Y,
Yamaguchi-Shinozaki
K,
Shinozaki K, Tran LS (2013) Sensing the environment: key roles of membrane-localized
kinases in plant perception and response to
abiotic stress. J Exp Bot 64(2):445–458
14. Rappsilber J, Ishihama Y, Mann M (2003) Stop
and go extraction tips for matrix-assisted laser
desorption/ionization, nanoelectrospray, and
LC/MS sample pretreatment in proteomics.
Anal Chem 75(3):663–670
15. Reiland S, Finazzi G, Endler A, Willig A,
Baerenfaller K, Grossmann J, Gerrits B et al
(2011)
Comparative
phosphoproteome
profiling reveals a function of the STN8 kinase
in fine-tuning of cyclic electron flow (CEF).
Proc Natl Acad Sci U S A 108
(31):12955–12960
16. Reiland S, Messerli G, Baerenf€ aller K,
Gerrits B, Endler A, Grossmann J,
Gruissem W, Baginsky S (2009) Large-scale
Arabidopsis
phosphoproteome
profiling
reveals novel chloroplast kinase substrates and
phosphorylation networks. Plant Physiol 150
(2):889–903
17. Rudashevskaya EL, Ye J, Jensen ON, Fuglsang
AT, Palmgren MG (2012) Phosphosite
mapping of P-type plasma membrane H+ATPase in homologous and heterologous
environments.
J
Biol
Chem
287
(7):4904–4913
450
Lin Xi et al.
unchanged; for analysis of modifications, such as phosphorylation, variable modifications need to be defined. In-depth information about MaxQuant settings is described in [22].
References
1. Benschop JJ, Mohammed S, O’Flaherty M,
Heck AJ, Slijper M, Menke FL (2007) Quantitative phospho-proteomics of early elicitor signalling in Arabidopsis. Mol Cell Proteomics 6
(7):1705–1713
2. Chen Y, Ho ¨henwarter W, Weckwerth W
(2010) Comparative analysis of phytohormone—responsive phosphoproteins in Arabidopsis thaliana using TiO 2 -phosphopeptide
enrichment and MAPA. Plant J 63(1):1–17
3. Chinchilla D, Zipfel C, Robatzek S,
Kemmerling B, Nurnberger T, Jones JD,
Felix G, Boller T (2007) A flagellin-induced
complex of the receptor FLS2 and BAK1 initiates
plant
defence.
Nature
448
(7152):497–500. https://doi.org/10.1038/
nature05999
4. Cox J, Mann M (2008) MaxQuant enables
high peptide identification rates, individualized
p.p.b.-range mass accuracies and proteomewide protein quantification. Nat Biotechnol
26(12):1367–1372.
https://doi.org/10.
1038/nbt.1511
5. Engelsberger WR, Schulze WX (2012) Nitrate
and ammonium lead to distinct global dynamic
phosphorylation patterns when resupplied to
nitrogen starved Arabidopsis seedlings. Plant J
69(6):978–995
6. Haruta M, Gray WM, Sussman MR (2015)
Regulation of the plasma membrane proton
pump (H(+)-ATPase) by phosphorylation.
Curr Opin Plant Biol 28:68–75. https://doi.
org/10.1016/j.pbi.2015.09.005
7. Kerk D, Bulgrien J, Smith DW, Barsam B,
Veretnik S, Gribskov M (2002) The complement of protein phosphatase catalytic subunits
encoded in the genome of Arabidopsis. Plant
Physiol 129(2):908–925. https://doi.org/10.
1104/pp.004002
8. Kim TW, Guan S, Sun Y, Deng Z, Tang W,
Shang JX, Sun Y, Burlingam A, Wang ZY
(2009) Brassinosteroid signal transduction
from cell-surface receptor kinases to nuclear
transcription factors. Nat Cell Biol 11
(10):1254–1260
9. Lan P, Li W, Wen TN, Schmidt W (2012)
Quantitative phosphoproteome profiling of
iron-deficient Arabidopsis roots. Plant Physiol
159(1):403–417
10. Marshall A, Aalen RB, Audenaert D,
Beeckman T, Broadley MR, Butenko MA,
Can ˜o-Delgado AI et al (2012) Tackling
drought stress: receptor-like kinases present
new approaches. Plant Cell 24(6):2262–2278
11. Menz J, Li Z, Schulze WX, Ludewig U (2016)
Early nitrogen-deprivation responses in Arabidopsis roots reveal distinct differences on transcriptome and (phospho-) proteome levels
between nitrate and ammonium nutrition.
Plant J 88(5):717–734. https://doi.org/10.
1111/tpj.13272
12. Niittyl€ a T, Fuglsang AT, Palmgren MG, Frommer WB, Schulze WX (2007) Temporal analysis of sucrose-induced phosphorylation
changes in plasma membrane proteins of Arabidopsis.
Mol
Cell
Proteomics
6
(10):1711–1726
13. Osakabe
Y,
Yamaguchi-Shinozaki
K,
Shinozaki K, Tran LS (2013) Sensing the environment: key roles of membrane-localized
kinases in plant perception and response to
abiotic stress. J Exp Bot 64(2):445–458
14. Rappsilber J, Ishihama Y, Mann M (2003) Stop
and go extraction tips for matrix-assisted laser
desorption/ionization, nanoelectrospray, and
LC/MS sample pretreatment in proteomics.
Anal Chem 75(3):663–670
15. Reiland S, Finazzi G, Endler A, Willig A,
Baerenfaller K, Grossmann J, Gerrits B et al
(2011)
Comparative
phosphoproteome
profiling reveals a function of the STN8 kinase
in fine-tuning of cyclic electron flow (CEF).
Proc Natl Acad Sci U S A 108
(31):12955–12960
16. Reiland S, Messerli G, Baerenf€ aller K,
Gerrits B, Endler A, Grossmann J,
Gruissem W, Baginsky S (2009) Large-scale
Arabidopsis
phosphoproteome
profiling
reveals novel chloroplast kinase substrates and
phosphorylation networks. Plant Physiol 150
(2):889–903
17. Rudashevskaya EL, Ye J, Jensen ON, Fuglsang
AT, Palmgren MG (2012) Phosphosite
mapping of P-type plasma membrane H+ATPase in homologous and heterologous
environments.
J
Biol
Chem
287
(7):4904–4913
450
Lin Xi et al.