Disclosed herein include systems, methods, compositions, and kits for sample identification and protein expression profiling. A sample indexing composition, or a composition for protein expression profiling, can comprise, for example, a protein binding aptamer associated with an oligonucleotide, such as a sample indexing oligonucleotide. Different oligonucleotides can have different sequences. Sample origin of cells, or protein expression profiles of cells, can be determined based on the sequences of the oligonucleotides by, for example, barcoding the oligonucleotides.