Table 1. The set of 26 Protocols supplied as part of the standard PiMS installation.

The Protocols are divided into groups reflecting the different stages of the protein-production pipeline. These Protocols are available to all users of a PiMS system. Users modify these Protocols by making a local copy of them and then making changes.

Protocol name	Input samples	Output samples
Processing DNA
PCR	Primers; template	PCR product
PCR cleanup	PCR product	PCR product
PCR product digest	PCR product	PCR product
Ligation	PCR product; linearized vector	Ligated plasmid
Bicistronic cloning	2× PCR product; vector	Recombinant plasmid
Bicistronic InFusion	2× PCR product; vector	Recombinant plasmid
Vector digest	Vector	Linearized vector
Clone verification	Template	PCR product
Cell growth and protein expression
Transformation	Plasmid; competent cells	Transformed cells
Culture	Transformed cells; culture medium	Transformed cells
Miniprep	Transformed cells	Purified plasmid
Trial expression	Plasmid	Protein
Large-scale expression	Plasmid	Pellet; supernatant
Solubilization	Pellet	Soluble protein
Processing protein samples
Tag cleavage	Soluble protein; enzyme	Soluble protein
Chromatography	Soluble protein	Soluble protein
Size-exclusion chromatography	Soluble protein	Soluble protein
Complexation	2× soluble protein	Soluble protein
Concentration	Soluble protein	Soluble protein
Protein characterization
Dynamic light scattering (DLS)	Soluble protein	—
Mass spectrometry	Soluble protein	—
Crystallography
Crystal screen	Soluble protein	Crystal
Crystal optimization	Soluble protein	Crystal
Crystal harvest	Crystal	Mounted crystal
Test diffraction	Mounted crystal	—
Diffraction	Mounted crystal	—