Table 1:
Summary of Instrumentation and Methods Used By Participants
| Report | Instrument | MS/MS Fragmentation | MS/MS Search Tool | FDR Estimation Tool | Phosphosite Localization Software | Quantitation Software | Enrichment Material |
|---|---|---|---|---|---|---|---|
| 01195 | Thermo Fusion | HCD | MaxQuant | MaxQuant <1% | MaxQuant | MaxQuant | unknown |
| 04345 | Thermo QE-HF | HCD | Proteome Discoverer (SEQUEST) | Percolator | ptmRS | Spectral Counting | TiO2 (GL Sciences) |
| 04704 | Thermo LTQ-OrbiXL | CID | MS-GF+ | n/a | LuciPHOr | MS peak intensity (in-house method) | TiO2 (GL Sciences) |
| 10104 | Thermo QE | HCD | PeptideShaker (X!Tandem) | PeptideShaker | PeptideShaker | Skyline | TiO2 (GL Sciences) |
| 11235 | Bruker Maxis HD UHR-TOF | CID | PEAKS | PEAKS <0.1% | PEAKS (AScore) | n/a | TiO2 |
| 12914 | Thermo QE-HF | HCD | MaxQuant | MaxQuant | MaxQuant | MaxQuant | unknown |
| 13273 | Thermo Lumos | HCD | MaxQuant | MaxQuant <1% | MaxQuant | MaxQuant | TiO2 (GL Sciences) |
| 13579 | Thermo QE-HFX | HCD | Proteome Discoverer (SEQUEST) | Percolator <1% | phosphorRS > 95% | Skyline | TiO2 (GL Sciences) |
| 23721 | Thermo QE-HFX | HCD | Proteome Discoverer | - | - | - | Fe(III)-NTA IMAC (AssayMap) |
| 23854-P238 | Thermo Lumos | HCD | Proteome Discoverer | - | - | - | unknown |
| 23854-P77 | Thermo Lumos | HCD | Proteome Discoverer | - | - | - | unknown |
| 26402 | Sciex 5600 | CID | Mascot | Mascot | Mascot | Skyline | TiO2 (GL Sciences) |
| 27573-Fusion | Thermo Fusion | CID | Proteome Discoverer (Mascot) | Percolator | ptmRS >75% | Minora | TiO2 (GL Sciences) |
| 27573-QEHF | Thermo QE-HFX | HCD | Proteome Discoverer (Mascot) | Percolator | ptmRS >75% | Minora | TiO2 (GL Sciences) |
| 30417 | Bruker amaZon/Impact | CID + ETD | Mascot | Mascot <5% | Mascot | Bruker Data Analysis | n/a |
| 31245 | Thermo QE-HFX | HCD | Comet | PeptideProphet | - | Skyline | n/a |
| 38060 | Thermo Fusion | CID, ETD, HCD | Mascot | Mascot <5% | Mascot | - | TiO2+ZrO2 (Glygen) |
| 66666 | Thermo Lumos | HCD | Comet | PeptideProphet | PTMProphet | TPP/Quantic | MagResyn Ti-IMAC, ResynBio |
| 81990 | Thermo QE-HF | HCD | Proteome Discoverer (Mascot) | Mascot | PhosphoRS (<1% FDR) | n/a | ERLIC |
| 84931 | Thermo QE | HCD | MaxQuant | MaxQuant | MaxQuant | MaxQuant | Ti4 (J&K Scientific) |
| 86749 | Thermo QE+ | HCD | PEAKS | PEAKS | PEAKS | - | TiO2 (Thermo) |
| 95051 | Agilent 6550 | CID + ECD | Byonic | Byonic <5% | - | - | Fe(III)-NTA IMAC (AssayMap) |
| 97867 | Thermo QE | HCD | MaxQuant | MaxQuant | MaxQuant | MaxQuant | Ti4 (MagResyn Ti-IMAC, ResynBio) |
| 99588 | Thermo Lumos | HCD | Mascot | Mascot <5% | Mascot | - | n/a |