Table 1:
Tolerance parameters used for comet search for each dataset
| Original dataset identifier | Tissue | Instrument | Count of .RAW files | Count MS2 spectra | Peptide mass tolerance (ppm) | Fragment tolerance (Da) | Count of observed sites reported | Statistical control method used (Peptides) | Statistical control method used (Sites) |
|---|---|---|---|---|---|---|---|---|---|
| PXD000923[27] | Flower | TripleTOF 5600 | 10 | 97388 | 20 | 0.02 | 2347 | ion score >34 (p<0.05) | Ascore>19, p≤0.01 |
| PXD002222[29] | Leaf | Q Exactive | 6 | 121117 | 20 | 0.02 | 2367 | filtered for peptide rank 1 and high identification confidence, corresponding to 1 % FDR Mascot score >20 | PhosphoRS probability >90%, in at least 2 of 3 biological replicates |
| PXD002756[34] | Anther | LTQ Orbitrap Elite | 5 | 225674 | 20 | 1.0005 | 8973 | Expectation value p<0.05 | phosphoRS (no threshold given) |
| PXD004705[33] | Leaf | Q Exactive | 9 | 208050 | 20 | 0.02 | 3412 | Protein Discoverer <1% FDR | PhosphoRS probability >90% in at least 2 of 3 biological replicates |
| PXD004939[31] | Leaf | Q Exactive | 9 | 212875 | 20 | 0.02 | 2271 | Protein Discoverer <1% FDR Mascot score >20 | PhosphoRS probability >90% |
| PXD005241[32] | Shoot, Leaf, Panicles (Young and Mature) | Q Exactive | 18 | 1040757 | 20 | 1.0005 | 5523 | Protein Discoverer <1% FDR | PhosphoRS probability >90% in at least 2 of 3 biological replicates |
| PXD012764[35] | Root | Q Exactive | 6 | 260560 | 10 | 0.02 | 2674 | Protein Discoverer <1% FDR | PhosphoRS score ≥50; PhosphoRS site probability ≥75% |
| PXD019291[38] | Pollen | Q Exactive | 4 | 110117 | 10 | 0.02 | 2246 | Not reported | Not reported |