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@ARTICLE{Arsova:851057,
      author       = {Arsova, Borjana and Watt, Michelle and Usadel, Björn},
      title        = {{M}onitoring of {P}lant {P}rotein {P}ost-translational
                      {M}odifications {U}sing {T}argeted {P}roteomics},
      journal      = {Frontiers in plant science},
      volume       = {Vol. 9},
      issn         = {1664-462X},
      address      = {Lausanne},
      publisher    = {Frontiers Media},
      reportid     = {FZJ-2018-04770},
      pages        = {1168},
      year         = {2018},
      abstract     = {Protein posttranslational modifications (PTMs) are among
                      the fastest and earliest of plant responses to changes in
                      the environment, making the mechanisms and dynamics of PTMs
                      an important area of plant science. One of the most studied
                      PTMs is protein phosphorylation. This review summarizes the
                      use of targeted proteomics for the elucidation of the
                      biological functioning of plant PTMs, and focuses primarily
                      on phosphorylation. Since phosphorylated peptides have a low
                      abundance, usually complex enrichment protocols are required
                      for their research. Initial identification is usually
                      performed with discovery phosphoproteomics, using high
                      sensitivity mass spectrometers, where as many
                      phosphopeptides are measured as possible. Once a PTM site is
                      identified, biological characterization can be addressed
                      with targeted proteomics. In targeted proteomics,
                      Selected/Multiple Reaction Monitoring (S/MRM) is
                      traditionally coupled to simple, standard protein digestion
                      protocols, often omitting the enrichment step, and relying
                      on triple-quadruple mass spectrometer. The use of synthetic
                      peptides as internal standards allows accurate
                      identification, avoiding cross-reactivity typical for some
                      antibody based approaches. Importantly, internal standards
                      allow absolute peptide quantitation, reported down to 0.1
                      femtomoles, also useful for determination of phospho-site
                      occupancy. S/MRM is advantageous in situations where
                      monitoring and diagnostics of peptide PTM status is needed
                      for many samples, as it has faster sample processing times,
                      higher throughput than other approaches, and excellent
                      quantitation and reproducibility. Furthermore, the number of
                      publicly available data-bases with plant PTM discovery data
                      is growing, facilitating selection of modified peptides and
                      design of targeted proteomics workflows. Recent instrument
                      developments result in faster scanning times, inclusion of
                      ion-trap instruments leading to parallel reaction
                      monitoring- which further facilitates S/MRM experimental
                      design. Finally, recent combination of data independent and
                      data dependent spectra acquisition means that in addition to
                      anticipated targeted data, spectra can now be queried for
                      unanticipated information. The potential for future
                      applications in plant biology is outlined.},
      cin          = {IBG-2},
      ddc          = {570},
      cid          = {I:(DE-Juel1)IBG-2-20101118},
      pnm          = {582 - Plant Science (POF3-582)},
      pid          = {G:(DE-HGF)POF3-582},
      typ          = {PUB:(DE-HGF)16},
      pubmed       = {pmid:30174677},
      UT           = {WOS:000441883100001},
      doi          = {10.3389/fpls.2018.01168},
      url          = {https://juser.fz-juelich.de/record/851057},
}