Reagent and consumable frequently asked questions for the Illumina Protein Prep (IPP)

Can serum and plasma samples be processed with the same kit?

• No, plasma samples must be used with Illumina Protein Prep Kit, Plasma, 96 reactions (Catalog 20137827), while serum samples must be used with Illumina Protein Prep Kit, Serum, 96 reactions (Catalog 20137828).

• Kits come with different: barcodes, calibrators (plasma or serum), diluent (plasma or serum), and QC samples (plasma or serum).

How many freeze-thaws cycles are accepted for Illumina reagents?

Up to three freeze-thaw cycles are permitted for the Illumina Protein Prep reagents.

Can different foil seals be used instead of the ones indicated?

Not recommended as different thicknesses have not been validated in the foil piercing procedures on deck.

Regarding the Matrix tubes, can another brand be used and, if so, how might they impact the assay? Are tubes included?

• Illumina has not tested any other type of matrix tubes. Labs can purchase these exact tubes loose, in a barcoded rack, or in a non-barcoded rack. Illumina recommends purchasing them in the barcoded racks (ThermoFisher Scientific, catalog # 3744-BR), because a 1D barcode on the rack is required for the end-to-end workflow.

• Other matrix tubes themselves have not been validated and could have different internal tube geometry which could result in poor sample transfer into the assay and therefore affect the results.

• No, the tubes are not included, labs must purchase them.

Is there a recommendation for how to store/re-use caps from the sample matrix rack to minimize cross-contamination if opt to re-freeze samples?

Caps can be replaced into the cap carrier. Additional caps can also be purchased from the vendor.

What are the 11 controls? What is their purpose?

The 11 controls in Illumina Protein Prep are:

• 3 blanks: provide an estimate of non-specific background in the assay.

• 5 calibrators: allow for the correction of plate-to-plate variability.

• 3 QC controls: provide a quality control check to determine if the plate performed as expected.

  
• • Note: Calibrators and QC samples are biologically very similar, both being pooled plasma or serum samples. Calibrators are used to perform normalization, which the QC samples are there to verify that the normalization calculations were successful in normalizing the assay.

• Additionally, there are SOMAmer Reagent Controls that are incorporated into each individual sample at know concentrations; which enable computing sample specific scale factors to normalize samples and assess quality.

Do the three dilution plates contain the same SOMAmers?

No, the three dilution plates contain different SOMAmers, but the same sample is used across the three plates.

When should the foil seals be removed from the SOMAmer-Bead dilution plates?

SOMAmer-Bead dilution plates are stable in indoor ambient lighting but sensitive to long-wave UV light. Cover with foil seal until loading onto the deck.

Why are there extra tips after an Illumina Protein Prep script?

This is expected. 7 stacks of 200 µl tips are loaded, but only 6 are consumed per E2E (end-to-end) run.

After how many runs should the liquid and solid waste be emptied?

Solid waste should be checked/emptied after each script.

Where can the reagent lot tacking information be found?

Reagent lots are tracked in log files found in:

C:\ProgramData\Illumina\ILASS-ProteinPrep\logs

For any feedback or questions regarding this article (Illumina Knowledge Article #9783), contact Illumina Technical Support [email protected].