Multiple marker abundance profiling: combining selected reaction monitoring and data-dependent acquisition for rapid estimation of organelle abundance in subcellular samples
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Multiple marker abundance profiling : combining selected reaction monitoring and data-dependent acquisition for rapid estimation of organelle abundance in subcellular samples. / Hooper, Cornelia M.; Stevens, Tim J.; Saukkonen, Anna; Castleden, Ian R.; Singh, Pragya; Mann, Gregory W.; Fabre, Bertrand; Ito, Jun; Deery, Michael J; Lilley, Kathryn S.; Petzold, Christopher J.; Millar, A. Harvey; Heazlewood, Joshua L.; Parsons, Harriet Tempé.
In: Plant Journal, Vol. 92, No. 6, 2017, p. 1202-1217.Research output: Contribution to journal › Journal article › Research › peer-review
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TY - JOUR
T1 - Multiple marker abundance profiling
T2 - combining selected reaction monitoring and data-dependent acquisition for rapid estimation of organelle abundance in subcellular samples
AU - Hooper, Cornelia M.
AU - Stevens, Tim J.
AU - Saukkonen, Anna
AU - Castleden, Ian R.
AU - Singh, Pragya
AU - Mann, Gregory W.
AU - Fabre, Bertrand
AU - Ito, Jun
AU - Deery, Michael J
AU - Lilley, Kathryn S.
AU - Petzold, Christopher J.
AU - Millar, A. Harvey
AU - Heazlewood, Joshua L.
AU - Parsons, Harriet Tempé
N1 - © 2017 The Authors The Plant Journal © 2017 John Wiley & Sons Ltd.
PY - 2017
Y1 - 2017
N2 - Measuring changes in protein or organelle abundance in the cell is an essential, but challenging aspect of cell biology. Frequently-used methods for determining organelle abundance typically rely on detection of a very few marker proteins, so are unsatisfactory. In silico estimates of protein abundances from publicly available protein spectra can provide useful standard abundance values but contain only data from tissue proteomes, and are not coupled to organelle localization data. A new protein abundance score, the normalized protein abundance scale (NPAS), expands on the number of scored proteins and the scoring accuracy of lower-abundance proteins in Arabidopsis. NPAS was combined with subcellular protein localization data, facilitating quantitative estimations of organelle abundance during routine experimental procedures. A suite of targeted proteomics markers for subcellular compartment markers was developed, enabling independent verification of in silico estimates for relative organelle abundance. Estimation of relative organelle abundance was found to be reproducible and consistent over a range of tissues and growth conditions. In silico abundance estimations and localization data have been combined into an online tool, multiple marker abundance profiling, available in the SUBA4 toolbox (http://suba.live).
AB - Measuring changes in protein or organelle abundance in the cell is an essential, but challenging aspect of cell biology. Frequently-used methods for determining organelle abundance typically rely on detection of a very few marker proteins, so are unsatisfactory. In silico estimates of protein abundances from publicly available protein spectra can provide useful standard abundance values but contain only data from tissue proteomes, and are not coupled to organelle localization data. A new protein abundance score, the normalized protein abundance scale (NPAS), expands on the number of scored proteins and the scoring accuracy of lower-abundance proteins in Arabidopsis. NPAS was combined with subcellular protein localization data, facilitating quantitative estimations of organelle abundance during routine experimental procedures. A suite of targeted proteomics markers for subcellular compartment markers was developed, enabling independent verification of in silico estimates for relative organelle abundance. Estimation of relative organelle abundance was found to be reproducible and consistent over a range of tissues and growth conditions. In silico abundance estimations and localization data have been combined into an online tool, multiple marker abundance profiling, available in the SUBA4 toolbox (http://suba.live).
U2 - 10.1111/tpj.13743
DO - 10.1111/tpj.13743
M3 - Journal article
C2 - 29024340
VL - 92
SP - 1202
EP - 1217
JO - Plant Journal
JF - Plant Journal
SN - 0960-7412
IS - 6
ER -
ID: 195464995