> For the complete documentation index, see [llms.txt](https://knowledge.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://knowledge.illumina.com/library-preparation/multiomics-library-prep/library-preparation-multiomics-library-prep-faq-list/000009799.md).
# 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](https://www.fishersci.fi/shop/products/matrix-screwtop-tube-caps-cap-trays-cap-inserts/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.
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| *For any feedback or questions regarding this article (Illumina Knowledge Article #9799), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000009799%20-%20Library%20Preparation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* |
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