Third Party equipment frequently asked questions for the Illumina Protein Prep Automation System (IPPAS)
What ancillary equipment is needed? (Note: quantities needed per 96 samples are listed in the Product Documentation.)
Equipment (or equivalents thereof):
Quad Microplate Shaker-Incubator Thermoshaker (VWR 97025-554)
8-channel screw cap decapper (Thermo 4105MAT)
Thermal cycler (Cole-Parmer EW-93945-12, EW-93945-22, EW-93945-02, OR Bio-Rad 12015392)
Axygen Silicone 96 Round Well Compression Flat Mat for Microplate (Fisher Scientific CM-FLAT)
DynaMag-2 Magnet (Thermo 12321D)
BioMicroLab Scan Barcode Reader (SPT LabTech, catalog # BMLScan)
BioMicroLab Thaw rack thawing station (SPT LabTech, catalog # BML-RTS)
BioShake XP - bench-top shaker (QInstruments, catalog # 1808-0505)
Optional: Biotek Cytation 5 Cell Imaging and Multimode Reader (Agilent CYT5MFAV-SN)
The customer should consult the Product Documentation for a full list of required equipment and consumables.
What are the vortex/shake and centrifuge settings during the automation protocol?
Script 1: Sample prep
PLASMADIL/SERUMDIL: centrifuge plate 280 x g for 15 seconds
Matrix Rack: centrifuge at 1000 x g for 1 minute
Binding: shake for 3.5 h at 28C at 850 rpm
Script 2: Proteomics Assay
Magnetic Beads: shake until resuspended (minimum 60 seconds)
MAGBEAD/MBPREP/MBBLOCK: if splashing, centrifuge at 280 x g for 15 seconds
Proteomics Probe Plate (PPP): shake at 1350 rpm for 1 minute, centrifuge at 280 x g for 15 seconds
Tag Reagent: vortex for 5 seconds
Hyb plate: shake at 1350 rpm for 1 minute, centrifuge at 280 x g for 15 seconds
Hybridization:
Hyb plate (if frozen): centrifuge at 280 x g for 15 seconds, replace seal, shake at 1350 rpm for 1 minute. If splashing occurs, centrifuge at 280 x g for 15 seconds
Script 3: Hyb Capture for NGS
Proteomics Amp Plate (PAP): once thawed, shake at 1350 rpm for 1 minute, centrifuge at 280 x g for 15 seconds
Indexes: once thawed, shake at 1350 rpm for 1 minute, centrifuge at 280 x g for 15 seconds
Proteomics Hyb Plate (PHP): once thawed, centrifuge at 280 x g for 15 seconds, shake at 1800 rpm for 3 minutes
Note: Index PCR until the end of the protocol are performed manually. Follow protocol guidance for shake/vortex and centrifugation steps.
How does the decapper work? What does it look like in action? Can the customer order more caps or another cap carrier?
The decapper looks similar to a multichannel pipette. It has square pegs that go into the square holes of the matrix sample tubes. It is strongly recommended to have one.
1 order of the decapper comes with 1 cap carrier. Labs can purchase additional cap carriers (Fisher 11577429, below), additional tubes, or caps if desired.
Is the shaker for SOMAmer binding step on-deck or off-deck? What does it look like?
The shaker is the Quad Microplate Shaker-Incubator Thermoshaker and it is off-deck.
Is a water bath required for reagents in 9.5k assay?
Yes, it is required, but not required for all components of the assay.
For any feedback or questions regarding this article (Illumina Knowledge Article #9799), contact Illumina Technical Support [email protected].
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