Before running an experiment, prepare your samples and add them to the appropriate wells in the kit input plate according to the loading instructions for the kit. For example, prepare the eight treatment-condition eukaryotic cell culture replicates that have more than 106 cells/mL each and the 8 control-condition replicates of the same cell density.


  1. Treat the biological input samples according to the appropriate protocols for the material and the field of study.
  2. Follow the kit instructions for:
  • Cell lysis, nuclease, and other appropriate protein-clearing instructions.
  • Determining the protein concentration of cleared cell lysates using established methods such as the Pierce™ BCA Protein Assay Kit (Product No. 23227) or Pierce™ Rapid Gold BCA Protein Assay Kit (Product No. A53226).
  • Use the input protein concentration to load the kit input plate.
  • Load the appropriate amount of protein into each well as defined by the kit’s capacity and the number of samples.
  • For example, the Thermo Scientific™ AccelerOme Label-free MS Sample Preparation Kit, 1 x 16 reactions (Label-free 16 kit) can processes 16 input samples, which must be in wells A1-A8 and B1-B8.
  • If you have fewer samples than the kit’s capacity in the plate within the same area, fill the first sample starting in the first row, going left to right. For example, to load 14 samples with the Label-free 16 kit, place the first eight in wells A1-A8, and the last six in wells B1-B6.
  • Label-free 16 kit
    Label-free 16 kit
    Label-free 16 kit with two empty wells
    Label-free 16 kit with two empty wells
  • NOTE

    If the input protein amount is outside the supported range for the kits, the results can be unreliable.

  • Load the kits on the trays according to the on-screen instructions.
  • Refer to the reagent kit guides for more details.
  • If you created an experiment method file in the Experiment Designer application and want to run these samples in an experiment using the file, see Run an experiment using a method file.

    If you want to use these samples in an experiment run without creating an experiment method file, that is, using a default method on the instrument, see Run an experiment using quick start .


    Flammable Material

    Do not put corrosive material or unauthorized chemicals or reagents into the system. This can cause chemical burns.


    Biological Hazard

    Do not use biohazardous and infectious materials like pathogen and prion samples. This can cause biological harm.