SWATH-MS-Based Proteomics: Strategies and Applications in Plants.

Most applied proteomic approaches require labeling steps. Recent technological advances provide an alternative label-free proteomics approach: SWATH-MS. This powerful tool is now widely used in animal studies but has drawn far less attention in plants. Here we summarize how this promising technology can be applied to facilitate functional analysis in plant research.

[1]  Ludovic C. Gillet,et al.  Data‐independent acquisition‐based SWATH‐MS for quantitative proteomics: a tutorial , 2018, Molecular systems biology.

[2]  Jian Wang,et al.  MSPLIT-DIA: sensitive peptide identification for data-independent acquisition , 2015, Nature Methods.

[3]  M. Dhaenens,et al.  Minimizing technical variation during sample preparation prior to label-free quantitative mass spectrometry. , 2015, Analytical biochemistry.

[4]  Moxian Chen,et al.  SWATH-MS Quantitative Proteomic Investigation Reveals a Role of Jasmonic Acid during Lead Response in Arabidopsis. , 2016, Journal of proteome research.

[5]  Wenqing Shui,et al.  Optimization of Acquisition and Data-Processing Parameters for Improved Proteomic Quantification by Sequential Window Acquisition of All Theoretical Fragment Ion Mass Spectrometry. , 2017, Journal of proteome research.

[6]  Ge-Fei Hao,et al.  Proteogenomic analysis reveals alternative splicing and translation as part of the abscisic acid response in Arabidopsis seedlings , 2017, The Plant journal : for cell and molecular biology.

[7]  Moxian Chen,et al.  SWATH-MS quantitative proteomic investigation of nitrogen starvation in Arabidopsis reveals new aspects of plant nitrogen stress responses. , 2018, Journal of proteomics.

[8]  Luc Garrigues,et al.  Assessment of SRM, MRM3, and DIA for the targeted analysis of phosphorylation dynamics in non‐small cell lung cancer , 2016, Proteomics.

[9]  Ruedi Aebersold,et al.  Mass-spectrometric exploration of proteome structure and function , 2016, Nature.

[10]  Hui Zhang,et al.  Analysis of dynamic protein carbonylation in rice embryo during germination through AP‐SWATH , 2016, Proteomics.

[11]  Ludovic C. Gillet,et al.  Targeted Data Extraction of the MS/MS Spectra Generated by Data-independent Acquisition: A New Concept for Consistent and Accurate Proteome Analysis* , 2012, Molecular & Cellular Proteomics.

[12]  Ruedi Aebersold,et al.  Complex‐centric proteome profiling by SEC‐SWATH‐MS , 2019, Nature Protocols.

[13]  A. Fernie,et al.  Full-Length Transcript-Based Proteogenomics of Rice Improves Its Genome and Proteome Annotation1 , 2019, Plant Physiology.

[14]  Ben C. Collins,et al.  Precise Temporal Profiling of Signaling Complexes in Primary Cells Using SWATH Mass Spectrometry , 2017, Cell reports.

[15]  David D. Shteynberg,et al.  Opening a SWATH Window on Posttranslational Modifications: Automated Pursuit of Modified Peptides* , 2015, Molecular & Cellular Proteomics.