Large-scale top-down proteomics of the Arabidopsis thaliana leaf and chloroplast proteomes.
Qianjie WangLiangliang SunPeter Knut LundquistPublished in: Proteomics (2022)
We present a large-scale top-down proteomics (TDP) study of plant leaf and chloroplast proteins, achieving the identification of over 4700 unique proteoforms. Using capillary zone electrophoresis coupled with tandem mass spectrometry analysis of offline size-exclusion chromatography fractions, we identify 3198 proteoforms for total leaf and 1836 proteoforms for chloroplast, with 1024 and 363 proteoforms having post-translational modifications, respectively. The electrophoretic mobility prediction of capillary zone electrophoresis allowed us to validate post-translational modifications that impact the charge state such as acetylation and phosphorylation. Identified modifications included Trp (di)oxidation events on six chloroplast proteins that may represent novel targets of singlet oxygen sensing. Furthermore, our TDP data provides direct experimental evidence of the N- and C-terminal residues of numerous mature proteoforms from chloroplast, mitochondria, endoplasmic reticulum, and other sub-cellular localizations. With this information, we suggest true transit peptide cleavage sites and correct sub-cellular localization signal predictions. This large-scale analysis illustrates the power of top-down proteoform identification of post-translational modifications and intact sequences that can benefit our understanding of both the structure and function of hundreds of plant proteins.
Keyphrases
- arabidopsis thaliana
- tandem mass spectrometry
- endoplasmic reticulum
- mass spectrometry
- liquid chromatography
- high performance liquid chromatography
- ultra high performance liquid chromatography
- gas chromatography
- simultaneous determination
- amyotrophic lateral sclerosis
- electronic health record
- machine learning
- high speed
- bioinformatics analysis
- cell death
- biofilm formation
- reactive oxygen species
- visible light
- staphylococcus aureus
- solar cells
- energy transfer
- data analysis