SorbiProt

How to read the SorgoProt data?

Sorghum cultivar RTx430 plants were grown under greenhouse conditions and the lower basal stem internodes were collected after 5 and 7 weeks after planting. Internode sections were embedded in HPMC/PVP embedding medium, flash frozen, and cryosectioned at 20 μm. Three cell-types were collected using laser capture microdissection (LCM), including vascular bundles (VB), sclerenchyma fibers (SF), and parenchyma (Par), as show in the picture above.

Captured tissues were processed using nanoPOTS on-chip protein extraction and trypin digested, and peptides were analyzed by nanoLC-MS/MS on an Orbitrap Fusion Lumos MS with FAIMS. Raw spectra were processed with FragPipe/MSFragger, validated with Philosopher, and quantified with IonQuant/MaxLFQ against the Sorghum bicolor UniProt proteome.

The tool provides protein abundances for each sampled tissue type, measured as MS peak areas of identified proteins in arbitrary units. Identifiers for searched proteins should use the Ensembl format “SORBI_3,”. Sorghum paralogs and ortholog proteins in Arabidopsis and other grass species are provided with each search. The dataset can be used to identify proteins enriched in VB, SF, or Parcells to explore pathways related to vascular development, cell wall formation, stress responses, among other biological processes.

How to download the raw dataset?

In this link (Excel file, size xx MB; CSV file, size XX MB)

Acknowledgements