Table 1.
The data sets from ProteomeXchange that were re-analysed, including brief details of the experimental protocols, and the search parameters and cutoff filter used in our PEAKS database searching.
| Species (tissue) |
Data set identifier | Phospho-peptide enrichment | Precursor mass error tol. | Fragment mass error tol. | Missed cleav-ages | Fixed modifications | Variable modifications | −10lgP thresholda | Instrument/fragmentation |
|---|---|---|---|---|---|---|---|---|---|
|
Arabidopsis thaliana (aerial parts) |
PXD000033 | IMAC and TiO2 | ±5.0 ppm | ±0.5 Da | Three | Beta-methylthiolation (+45.99 Da), iTRAQ 4plex (K, N-term) (+144.10 Da) | Oxidation (M) (+15.99 Da), Phosphorylation (STY) (+79.97 Da), Acetylation (N-term) (+42.01 Da), Deamidation (NQ) (+0.98 Da), iTRAQ 4plex (Y) (+144.10 Da) | 30 | Orbitrap (Orbi-Trap) CID/HCD |
|
Arabidopsis thaliana (leaves) |
PXD000421 | MOAC | ±7.0 ppm | ±0.8 Da | Two | Carbamidomethylation (+57.02 Da) | Oxidation (M) (+15.99 Da), Phosphorylation (STY) (+79.97 Da), Acetylation (N-term) (+42.01 Da), Deamidation (NQ) (+0.98 Da) | 24.2 | Orbitrap (Orbi-Trap) CID |
|
Oryza sativa Indica (leaves) |
PXD002222 | TiO2 | ±20.0 ppm | ±0.05 Da | One | Carbamidomethylation (+57.02 Da) | Oxidation (M) (+15.99 Da), Phosphorylation (STY) (+79.97 Da), Acetylation (N-term) (+42.01 Da) | 19 | Orbitrap (Orbi-Trap) HCD |
|
Oryza sativa Indica (pistil) |
PXD000923 | IMAC | ±15 ppm | ±0.05 Da | One | Carbamidomethylation (+57.02 Da) | Oxidation (M) (+15.99 Da), Phosphorylation (STY) (+79.97 Da) | 21 | Triple TOF HCD |
MOAC = Metal Oxide Affinity Chromatography; IMAC = Immobilized Metal Affinity Chromatography.
a
PEAKS DB’s −10lgP threshold score was set as a cutoff filter to achieve false discovery rate (FDR) of 1.0% at the peptide sequence level.