Scoring models¶
andes picks a model by (activation, instrument, enzyme, protocol), automatically for mzML,
.raw and .d. --fragmentation is needed only for MGF; --protocol
<auto\|TMT\|iTRAQ\|iTRAQ-phospho\|phospho\|standard> selects a labelled or enriched model;
--model <slug> loads one model by id (e.g. hcd_qexactive_tryp_tmt). The enzyme comes from
--enzyme (default trypsin). An uncovered regime uses the nearest model.
Supported models¶
All 17 models are trained by andes on public PRIDE data; the store contains no MS-GF+-derived model data.
model_id |
activation / instrument / enzyme / protocol | Training data (public PRIDE) | Benchmark |
|---|---|---|---|
hcd_astral_tryp |
HCD / OrbitrapAstral / Trypsin / Automatic | PXD046453 | Astral |
hcd_qexactive_tryp |
HCD / QExactive / Trypsin / Automatic | ProteomeTools (PXD009449) | global default model |
hcd_qexactive_tryp_tmt |
HCD / QExactive / Trypsin / TMT | PXD010429 | — |
hcd_qexactive_tryp_itraq |
HCD / QExactive / Trypsin / iTRAQ | public PRIDE (see manifest) | — |
hcd_qexactive_tryp_phosphorylation |
HCD / QExactive / Trypsin / Phosphorylation | public PRIDE (see manifest) | — |
hcd_highres_tryp_tmt |
HCD / HighRes / Trypsin / TMT | PXD010429 | — |
hcd_highres_nocleavage |
HCD / HighRes / NoCleavage / Automatic | ProteomeTools (PXD009449) | — |
hcd_highres_nocleavage_phosphorylation |
HCD / HighRes / NoCleavage / Phosphorylation | ProteomeTools (PXD009449) | — |
cid_lowres_tryp |
CID / LowRes / Trypsin / Automatic | PXD009875 + PXD000865 | UPS1 (low-res) |
cid_lowres_tryp_tmt |
CID / LowRes / Trypsin / TMT | PXD016999 + PXD014502 + PXD017092 | TMT a05058 (low-res) |
cid_lowres_lysc |
CID / LowRes / LysC / Automatic | PXD000865 | ⚠ limited training data |
cid_lowres_argc |
CID / LowRes / ArgC / Automatic | public PRIDE (see manifest) | ⚠ limited training data |
cid_lowres_gluc |
CID / LowRes / GluC / Automatic | public PRIDE (see manifest) | ⚠ limited training data |
etd_highres_tryp |
ETD / HighRes / Trypsin / Automatic | public PRIDE (see manifest) | — |
etd_highres_tryp_phosphorylation |
ETD / HighRes / Trypsin / Phosphorylation | public PRIDE (see manifest) | — |
etd_lowres_tryp_phosphorylation |
ETD / LowRes / Trypsin / Phosphorylation | public PRIDE (see manifest) | — |
uvpd_qexactive_tryp |
UVPD / QExactive / Trypsin / Automatic | public PRIDE (see manifest) | — |
"see manifest": the accession is tracked in the training manifest, not yet pinned here. ⚠ limited training data: few PSMs were available, so treat these models as best-effort.
To train your own, see TRAIN.md.