Techniques¶
What the modelled part of XFP is designed to do, as intent. First cut.
A technique is a portable Catalog Method; a Practice is how a facility adapts it. XFP does one technique, X-ray footprinting, in two delivery modes: static / capillary-flow, and shutterless high-throughput. The Method below renders unlinked and is carried pending until the owner-scope decision (TECH-1) brings it into the catalog.
| Technique | Catalog method | Notes |
|---|---|---|
| X-ray footprinting (capillary-flow / static) | x_ray_footprinting |
gate a timed white-beam dose onto a flowing solution capillary or flow-cell sample, recording exposure time x flux x attenuation as the delivered dose; the fleet's first dose-delivery Method, new to the catalog; readout is offline mass spec (TECH-1, READOUT-1) |
| High-throughput footprinting (HTFly) | x_ray_footprinting |
sweep a fly-cell row through the defining slit at a set stage velocity so the exposure (dose) is the slit gap over the velocity, across a 96-well plate; the same x_ray_footprinting Method with the HTFly stage as the dose-timing (TECH-1, HT-1) |
Both modes need the white-beam chain (the mirror, the slits, the Al filter wheel for dose rate), the dose gating (the timed shutters or the delay-generator-fired Uniblitz, or the HTFly velocity), the sample side (a stage and the delivery pump), and the flux monitors (to record the delivered dose). They differ only in how the exposure is timed and how many samples are handled.
The technique is dose delivery, and the readout is offline¶
This is the heart of what makes XFP a new shape for CORA. X-ray footprinting is not a measurement technique in the sense the rest of the fleet uses: the beamline does not record a structural signal. It delivers a controlled radiolytic dose to a biological macromolecule in solution, generating hydroxyl radicals that covalently modify the molecule at solvent-accessible sites. The modified sample is then analysed offline by mass spectrometry, which reveals which residues were exposed and thus maps the molecule's surface and conformational changes.
So the Method x_ray_footprinting is a dose-delivery Method:
- its controlled variable is the delivered dose (exposure time times flux times attenuation), not a detector setting;
- its product is a footprinted sample plus a dose record, not a measurement frame;
- its structural readout is the offline-readout seam (mass spec, downstream and off the beamline,
READOUT-1).
That is why x_ray_footprinting is proposed as a Method distinct from anything in the catalog: not because the optics are unusual (a white beam, a filter, a shutter), but because the experiment shape, dose-in, sample-out, structure-read-elsewhere, is genuinely new. Whether the catalog ultimately holds a x_ray_footprinting Capability, or a broader "controlled-dose / irradiation" Capability with footprinting as a Practice adaptation, is the owner-scope decision (TECH-1); XFP records the case, it does not mint the vocabulary. The matching Site Practices (XFP_footprinting_practice, XFP_high_throughput_footprinting_practice) are carried pending in the NSLS-II Site; each binding lands when its Capability does.
A time-resolved mode, deferred¶
The profile collection also contains a time-resolved capillary-flow mode (a stopped-flow style mixing experiment before irradiation), but it is flagged unfinished in the source, so no Practice is recorded for it here; it is a later mode that would reuse the same x_ray_footprinting Method with a mixing step in the Procedure (TECH-1).
Not modelled yet¶
The concrete acquisition recipes are not written yet. For footprinting that is the dose series (the set of exposure times or filter thicknesses that build a dose-response curve), the flow program that presents fresh sample, the aliquot-collection pattern, and the flux-to-absorbed-dose calibration that converts the measured flux to the dose the sample received (a seam constant that lives in offline analysis, DOSE-1). The downstream linkage to the offline mass-spec result is the offline-readout seam, not a beamline recipe (READOUT-1). These join as the deployment approaches the point where CORA drives XFP.
Whether x_ray_footprinting enters CORA's catalog is an owner-scope decision on Model: a modelling exercise reinforces the case but does not mint cross-facility Method vocabulary on its own. See Open questions for the world-facts to confirm first.