Table 1.

Main sample preparation methods used in single-cell proteomics.

Sample Preparation Methods	Description
	Protocol	Advantages
Filter-Aided Sample Preparation (FASP)	Proteins are retained in a filter membrane and are accessible for enzymatic digestion. The generated peptides are collected by centrifugation.	This technique allows the removal of SDS and other low-molecular weight contaminants.
in-StageTip digestion (iST)	Complete sample preparation performed in a StageTip. The final peptide is picked by solid-phase extraction.	It avoids the filter membrane.
Single-Pot Solid-Phase enhanced Sample Preparation (SP3)	It is carried out using functionalized paramagnetic beads to trap peptides within a magnetic field.	Efficient removal of contaminants by washing with different organic solvents.
Minimal ProteOmic sample Preparation (mPOP)	MS compatible digestion buffer which eliminates cleanup steps and minimizes the sample volume used.	It makes it possible to automate sample preparation with PCR thermocyclers, enabling processing many samples in parallel.
Automated nano-ProteOmic sample Preparation (nPOP)	It uses a piezo acoustic device to isolate individual cells using small volumes.	It is a miniaturized and massively parallel method for high throughput.