You have to have a freeze dryer that actively freezes the sample on a shelf before applying the vacuum, and then keep the sample frozen with the shelf. If you have a basic lab model (flasks and a tree) I think that this will not work well even if you pre freeze the sample.

Things to watch out for:

If you use plastic ware to contain the sample, sometimes injection moulded plastics have things in the plastic or chemicals used in the production process (waxes or silicones to help the plastic part com off the mould) that will affect the drying process

pH shift when freezing a buffer salt, phosphate buffers can be especially prone to this.

Kind regards