Learn! Access our knowledge bank

Yes, the condensation in the Tray Cooler can be reduced. Since the Tray Cooler can cool down to 20°C below the surrounding temperature, higher temperature differences will cause more condensation. To minimize this, place the Tray cooler in a room with air conditioning, low humidity, and avoid direct sunlight.

a. You can skip the LYSE and DIGEST steps by de-selecting them when editing the method. However, samples must first be processed using iST or iST-BCT.

b. It is also possible to do Digest & Cleanup and perform the lysis step offboard, e.g., if you prefer different lysis conditions.

This error occurs when the method is still assigned to a Job. For safety reasons, methods cannot be deleted while in use. To delete a method, first delete all Jobs, and then you will be able to remove it.

This takes roughly 1.5 hours, depending on the surrounding temperature. If needed, you can leave the system running for extended periods, such as overnight, to have it ready for use early the next day.

Yes, you can start a run in the afternoon and collect your eluted peptides the next morning, for example. In this case, please make sure you use the cooled elution position.

After approximately 15 hours of overnight storage in the ELUTE buffer, protein and peptide identifications remain comparable, and no significant increase in deamidation rates was observed.

Based on our internal tests, there is no significant quality loss between samples 1 and 96. Differences in protein/peptide identifications or other QC parameters are negligible, ensuring consistent result quality across all 96 samples.

The automated processing times (h:mm) from lysis to eluted peptides are 3:40, 5:10, and 8:12 for 24, 48, and 96 samples, respectively.

We recommend transferring cell pellets to the provided Deepwell SAMPLE PLATE. A dedicated Deepwell plate adapter is fixed on the thermal mixer. A standard 96-well cell culture plate would not accommodate sufficient volume for the iST workflow, would not fit the thermal shaker adapter, and would fall outside the optimized calibration points.

The protein input range is  1–100 µg.

For the BeatBox Tissue Kit 96x, the recommended wet weight of tissue is from 1 to 5 mg.

For the BeatBox Tissue Kit 24x, the recommended wet weight of tissue is from 5 to 50 mg.

Cell count is based on the OD read out. Our recommendation for the BeatBox Tissue Kit 96x would be to use:

- yeast cells, 0.6 OD600, 1 mL volume

- bacteria cells, 0.5 OD600, 1 mL volume

- 6e5 mammalian cells

For the BeatBox Tissue Kit 24x, up to 1e7 mammalian cells can be used.

We recommend a volume range from 50 to 100 µL of LYSE buffer or your own lysis buffer per well in the BeatBox Tissue Kit 96x.

If you want to decrease the buffer volume for very low sample inputs containing 1-20 µg protein, please contact us via info@preomics.com for a modified protocol.

For the BeatBox Tissue Kit 24x, we recommend 300 to 1000 µL. To create optimal conditions, buffer to sample ratios should be adjusted individually. Lower buffer volumes down to 100 µL are possible but recovering the full sample volume may be difficult for foamy or highly concentrated homogenates.

‍

BeatBox homogenizes various tissue types, from softer tissues, such as the brain, to more fibrous tissues, such as cardiac muscle. Tissue can be collected from different organisms, e.g. human, rat, mouse, plant.For hard tissues, such as bone, skin, nails, and hair, protein extraction efficiency is relatively low and requires multiple runs with BeatBox. For bone samples, demineralization prior to homogenization is necessary.

All cell types from procaryotic to eucaryotic cells. When yeast is used, it is recommended that prior to homogenization, the cell slurry is heated for 10 min at 95 °C to break the cell walls.

For the BeatBox Tissue Kit 96x, we recommend a maximum of 500 µg of total protein and 5 mg of wet weight for tissue samples. The amount of extracted proteins per mg of tissue wet weight will depend on the tissue type. For cell samples, we recommend a maximum of 100 µg of total protein amount. See FAQ 2.1 for approximate starting amounts corresponding to 100 µg protein.

For low protein input amounts of 1-20 µg, please contact us via info@preomics.com for a modified protocol.

This will depend on the tissue type and amount; we recommend a minimum of 5 minutes. In general, softer tissues and smaller tissue amounts will be completely homogenized in one run of 10 min with standard settings. Highly fibrous tissues or bigger tissue chunks may need additional or longer runs for complete homogenization.

Yes, BeatBox can homogenize FFPE tissue. For a dedicated protocol and more information, please visit: https://www.preomics.com/applications/ffpe. FAQs related to this protocol are collected in section 12.

Yes, you can use your own lysis buffers.  In general, we recommend LYSE buffer from the PreOmics portfolio or RIPA buffer, since we obtained very good results in terms of protein extraction efficiency in our in-house tests. If you are using your own lysis buffer, you can continue with your in-house sample preparation or with PreOmics kits (subject to composition compatibility – for recommendations and limitations, see FAQ 1.1).

NOTE: If you want to freeze surplus homogenate prepared with the BeatBox Tissue Kit 24x, we recommend using RIPA buffer or SP3-LYSE for lysis and subsequent storage. The PreOmics’ iST-LYSE buffer is incompatible with freezing of tissue homogenates/cell lysates in BeatBox TUBES due to increased protein amounts.

Yes, you can use samples that have been stored at -80 ºC. Samples should be thawed on ice before adding lysis buffer. We recommend keeping deep-frozen samples on ice before adding lysis buffer. If you want to freeze samples in the 96w PLATE or the TUBES, do not use liquid nitrogen.

NOTE: PreOmics LYSE buffer’s efficiency to lyse, reduce and alkylate sample rapidly decreases when used below room temperature.

Yes, this is possible. It is very important to spin down the BeatBox 96w PLATE at 300-500 rcf for 30-60 sec before removing the SILICONE MAT to avoid cross-contamination. If SP3 LYSE or high concentrations of SDS have been used in your own lysis buffer, a longer spin down time is recommended to decrease the foam, before transferring samples to clean tubes/plate.

The same applies to the BeatBox TUBES from the BeatBox Tissue Kit 24x. Here, we recommend a spin down at 1500 rcf for 30-60 sec.

NOTE: Please do not exceed the following max. centrifugation speeds to avoid plate/tube breakage and sample loss:

- BeatBox 96w PLATE with GYUTO BEAD in swing-bucket rotor: 500 rcf

- BeatBox 96w PLATE without GYUTO BEAD in swing-bucket rotor: 2250 rcf

- BeatBox TUBES with GYUTO BEAD: 1500 rcf

- BeatBox TUBES without GYUTO BEAD: 18000 rcf

Use a suitable plate carrier together with the swing-bucket rotor, e.g. PCR plate adapter Eppendorf #5825711009 for Eppendorf plate rotors.

For the BeatBox Tissue Kit 96x, place the BeatBox 96w PLATE onto a GYUTO BEADS COLLECTION RACK after the homogenization process and centrifugation step. This will pull the beads to the side, and you can then transfer the homogenate by pipetting it into a new reaction vessel/plate. For high throughput applications, we recommend using a multi-channel pipet to reduce the processing time.

For the BeatBox Tissue Kit 24x, spin down the BeatBox TUBES (1500 xg, 30-60 sec) after homogenization and transfer the homogenate using a pipet.

This is proprietary information that cannot be shared.

The GYUTO BEAD is coated with a surface material that has been designed to prevent protein binding.

The BeatBox does not have heating or cooling options. The BeatBox operates at room temperature. For workflows that require cooling during homogenization, samples can be temporarily cooled with cooling racks from other suppliers. Please contact us at info@preomics.com for more information.

Unfortunately, this is not possible. The BeatBox should be operated at an ambient temperature of 18-28 °C. For workflows that require cooling during homogenization, samples can be temporarily cooled with cooling racks from other suppliers. Please contact us at info@preomics.com for more information.

During homogenization, the BeatBox operates with minimal heat induction. The temperature of the sample will therefore remain stable at room temperature during the homogenization process.

NOTE: Phosphatase inhibitor cocktails can be added into the PreOmics’ LYSE if needed. For recommendations regarding protease inhibitors, please have a look at FAQ 1.4.

Yes, the BeatBox 96w PLATE containing samples can be heated up to 95 ºC. The maximum time is 6 hours. To avoid SILICONE MAT peeling caused by temperature, we recommend to use a ThermoCycler/PCR Cycler with a heated lid exerting pressure from the top. Alternatively, close the 96w PLATE with cap strips (Eppendorf #0030124847).

NOTE: Spin down the BeatBox 96w PLATE before removing SILICONE MAT to prevent cross-contamination. We recommend to centrifuge the plate for 30-60 seconds at amax. speed of 500 xg.

BeatBox employs a proprietary technology which homogenizes samples differently in comparison to sonication or bead beating. The highly efficient homogenization is based on the movement of a single magnetic particle, called GYUTO BEAD, in an alternating magnetic field inside a reaction vessel and the resulting disruption of tissues and cells within the sample to be homogenized.

In contrast to bead mills, the only moving part of the BeatBox is the GYUTO BEAD in the plate well or tube. This innovative technology minimizes heat induction in the sample, thereby negating the need for sample cooling.

The BeatBox settings of low, standard, and high refer to the power of homogenization and the speed or “intensity” of the GYUTO BEAD movement in the well. The precise mechanism underlying this movement is proprietary.

We recommend starting with the standard setting, which is generally sufficient to completely homogenize softer tissues within 10 min. Harder or highly fibrous tissues may need additional or longer runs and/or the high setting for complete homogenization.

The supplied BeatBox PLATE is optimized to work with the GYUTO BEAD.  Homogenization efficiency can be affected if the plate used does not have the correct dimensions. The ratios between the GYUTO BEAD:volume:well shape/size is critical to efficient homogenization and although another plate may appear similar, individual dimensions may not be. PreOmics can recommend alternative plates. Please contact us via info@preomics.com However, PreOmics will not support any issues with possible cross-contamination, leaching or loss of samples, when switching to a different plate or when transferring the GYUTO BEAD.

The BeatBox is not compatible with 1.5 mL tubes that have a conical shape, e.g., Eppendorf # 0030120086. The ratios between the GYUTO BEAD:volume:well shape/size are critical to efficient homogenization and have been optimized for the 2 mL tube supplied with the PreOmics kit. PreOmics can recommend alternative 2 mL tubes. Please contact us via info@preomics.com. However, PreOmics will not support any issues with possible cross-contamination, leaching or loss of samples, when switching to different tubes or when transferring the GYUTO BEAD.

The BeatBox has been designed primarily for proteomics and each part of the kits is compatible with common lysis buffers used in these workflows.

However, the BeatBox can also be used for other omics applications, such as metabolomics or lipidomics. Depending on the application, the extraction buffer or solvent may vary. The following compositions are generally compatible with the BeatBox kits:  

• aqueous buffers with a maximum of 5% SDS
• organic solvents: methanol or isopropanol (up to 80% in water or acetonitrile)

Other organic solvents commonly used in metabolomics, such as chloroform, MTBE, or ethyl acetate are incompatible with the plastic ware of the BeatBox kits. For further information, please contact us at info@preomics.com.

Yes, this is possible after the GYUTO BEADS have been removed from the wells. Simultaneous removal of all 96 GYUTO BEADS can be done with help of the BeatBox bead remover. Please contact us for more details via info@preomics.com.

When PreOmics LYSE buffer is used, we recommend using the Pierce™ BCA Protein Assay Kit - Reducing Agent Compatible or the NanoOrange™ Protein Quantitation Kit (Thermo Fisher Scientific), depending on which LYSE is used. Some assays require dilution with distilled water to achieve the best results, please see FAQ 1.7. for more information.  If using your own lysis buffers, be aware of any of the maximum concentrations and their compatibility with the assay of choice.  Again, dilution may be needed to prevent interference of the readout.

For the protein quantification step, mix the tissue homogenate/cell lysate by pipetting, transfer an appropriate amount of mixture to the new reaction vessel and centrifuge at 10 000 xg to pellet the debris. The clear supernatant can be used for protein quantification.

The only thing that moves during the process is the GYUTO BEAD.

No polymer contamination has been observed by LC-MS of tryptic digests of samples, which were prepared with the BeatBox Tissue kit 96x in combination with the iST family of sample preparation kits. The GYUTO BEAD has a special bead-coating to prevent protein binding during sample preparation and the SILICONE MAT and PLATE are resistant to the ingredients of the LYSE buffer, thus eliminating the risk of any contamination/leaching occurring from these sources.

The number of samples per run can be freely selected by the user, e.g.  1x 96 samples, or 4x 24 samples. However, each well and GYUTO BEAD can be used only once, and it is recommended not to run the BeatBox 96w PLATE more than 40 minutes in total (independent of the setting).

NOTE: Do not remove the GYUTO BEADS from used wells; transfer only the homogenate/lysate for downstream steps.

You can run the BeatBox 96w PLATE with samples multiple times, but it is not recommended to exceed 40 minutes in total (independent of the settings). The number of runs depends on the hardness of the tissue.

NOTE: You can increase the power of homogenization in the additional runs. E.g., from STANDARD to HIGH setting.

Yes, there is no need to centrifuge the homogenate. PreOmics’ kits are designed to work with tissue homogenate/cell lysate. Before proceeding with PreOmics’ DIGEST step, estimate the protein content of the homogenate and transfer only the volume that contains approx. 100 µg of protein.

NOTE 1: For protein quantitation assays use only clear supernatant. Take a homogenate aliquot and centrifuge with >10 000 xg for 15 mins to remove cell or tissue debris.

NOTE 2: If you are using your own lysis buffer, you can also continue with PreOmics kits (subject to composition compatibility – for recommendations and limitations, see FAQ 1.1).

Yes, the BeatBox Tubes can be frozen (-20 °C and -80 °C) with tissue samples, with or without lysis buffer, and before or after homogenization.  Please follow the instructions for use for Eppendorf Safe-Lock Tubes and do not use the tubes with liquid nitrogen.

NOTE: PreOmics’ iST LYSE buffer is incompatible with freezing of tissue homogenates/cell lysates in TUBES due to increased protein amounts. As alternative, we recommend using RIPA buffer or SP3 LYSE for lysis and subsequent storage.

Yes, it is possible to remove all 96 GYUTO BEADS simultaneously with help of the BeatBox bead remover. Please contact us for more details via info@preomics.com. If you only want to process a few samples, we recommend instead to transfer the homogenate from the BeatBox 96w PLATE to a fresh sample vessel.

In principle, the GYUTO BEAD can be present in the homogenate for further sample preparation, such as digestion. However, please keep in mind that the max. well volume of 150 µL is small and incompatible with the PreOmics’ kit workflows. For practical reasons, we therefore recommend transferring the homogenate/lysate to a fresh sample vessel before continuing with the next sample prep step.

The BeatBox plate adapter is only compatible with the 96w PLATE and not with single 0.2/0.5 mL tubes. Certain types of 0.5 mL tubes are compatible with the BeatBox tube adapter and certain types of 0.2 mL tubes are compatible with the BeatBox plate adapter when placed into a suitable tube rack. Please contact us via info@preomics.com for more information. However, PreOmics will not support any issues with possible cross-contamination, leaching or loss of samples, when switching to different tubes or when transferring the GYUTO BEAD.

Increased sample viscosity after tissue homogenization or cell lysis is often caused by DNA released from the nuclei. Since BeatBox only minimally shears DNA, we recommend to break down DNA through addition of nucleases or sonication. This should reduce sample viscosity.  

Nucleases like Benzonase are compatible with all PreOmics’ LYSE buffers. Please mix the enzyme directly with the LYSE buffer, add the mix to your samples and continue with sample homogenization in the BeatBox. For further recommendations on nuclease amounts, see FAQ 1.25.

The BeatBox bead remover is only compatible with the BeatBox 96w PLATE and the corresponding GYUTO BEAD COLLECTION RACK from the accessory box. We do not recommend using it together with other plates.

No polymer contamination has been observed by LC-MS of tryptic peptides and corresponding buffer controls. Samples were prepared with the BeatBox 96w kit, followed by removal of the GYUTO BEADS with the BeatBox bead remover and bead remover foil, and digestion and peptide clean-up with the iST family of sample preparation kits. The BeatBox bead remover foil is a single-use consumable that is resistant to the ingredients of the LYSE buffer, thus eliminating the risk of any contamination/leaching occurring from these sources.

This is not recommended. PreOmics will not support any issues with possible cross-contamination or leaching when switching to a different film or foil. The supplied BeatBox bead remover foil is optimized to work with the BeatBox bead remover. Other less elastic films or foils are likely pierced during the removal procedure, leading to contamination of the tool.

In case of contamination of these items with sample, you can clean them by disinfectant wipe down using a damp cloth with the following substances: 70% ethanol, 70% isopropanol, 10% sodium hypochlorite, aldehyde-based disinfectants. Please refer to the BeatBox user manual for details.