Protein related analysis, including protein identification, protein quantification and protein structure analysis is a significant process for a successful experiment. In this article, we will introduce several protein identification methods such as protein sequence analysis, peptide mass fingerprinting and shotgun proteomics for scientists’ reference.
Protein sequence analysis
Protein sequence analysis, also known as de novo protein sequence analysis, which is a method in which a peptide amino acid sequence is determined from tandem mass spectrometry in mass spectrometry field. During its workflow, there is no need for the assistance of sequence database. However, the de novo sequencing was thought to be slow, it is mostly used when the protein database was unavailable.
Peptide mass fingerprinting
Peptide mass fingerprinting, also known as protein fingerprinting, is an ideal analytical technique for protein identification. The most effective method in PMF for identifying protein is MALDI-TOF mass spectrometry, which is famous for its rapid and sensitive identification of proteins by peptide mass fingerprinting. In addition, two-dimensional gel electrophoresis, SDS-PAGE and liquid chromatography are also widely used in many laboratories.
Shotgun proteomics is based on identification and quantification of peptides from digested proteins by using tandem mass spectrometry. It refers to the use of bottom-up proteomics techniques in protein identification by using a combination of high performance liquid chromatography combined with mass spectrometry. The technique can allow global protein identification as well as the ability to profile dynamic proteomes. What’s more, it can avoid the modest separation efficiency and poor mass spectral sensitivity associated with intact protein analysis.
In addition to these technologies listed here, there are still many other methods for protein identification and protein quantification fields. The most effective one should be up to the proper process and sample preparation.