While most often scientists use DNA to accurately identify people in a wide variety of situations ranging from paternity testing to human remains identification and criminal investigations, proteins are more resistant to exposure to destructive chemicals. Also, DNA stays the same across all tissues and cells in the human body.

This isn’t the same for proteins. They vary depending on what tissue or body fluid they come from. This makes protein identification analysis a promising technique for identifying tissues that contribute biological material.

Keep reading to learn how tandem mass spectrometry is helpful for protein identification and analysis in forensics and healthcare.

What Is Tandem Mass Spectrometry?

Mass spectrometry is a technique that provides valuable insights into the structure and mass of entire molecules or molecular fragments. This is made possible by a mass spectrometer, a sophisticated device comprising an ion source, a mass analyzer, and a detector. The ion source generates ions, the mass analyzer sorts these ions based on their mass-to-charge ratio, and the detector measures the abundance of each ion, completing the process.

Tandem mass spectrometry (MS/MS) is a two-step technique. Scientists use interconnected mass spectrometers for it. A particular set of ions is separated from the other ions coming from the ion source. These ions are then fragmented by a chemical reaction in the first stage of MS/MS. Mass spectra for the fragments are generated in the second stage. MS/MS fragments proteins and peptides to determine the amino acid sequence of proteins and peptides.

The Use of MS/MS In Protein Identification

Protein identification is the process of screening and identifying proteins. There are two main approaches for MS/MS in protein identification: top-down, which is an analysis of intact proteins,  and bottom-up which analyzes proteins that were digested into peptides beforehand.

How Does MS/MS Work?

The process begins with sample preparation, which includes washing with phosphate-buffered saline (PBS) to remove contaminants from the sample. The extraction of proteins for analysis is performed via chemical lysis and, in some cases, solubilization, which breaks the cells and releases proteins.

After sample preparation, the peptide mixture is ionized to separate the peptides, which serve as unique identifiers of the protein’s fingerprint. MS/MS spectra of each peptide are used to search protein databases for matched peptides to identify proteins.


Tandem mass spectrometry is useful not only in forensics but also in healthcare. It sheds light on how molecular mechanisms differ between healthy and diseased states. It also helps identify specific proteins in various tissues based on their biological functions.

Tandem MS is also helpful in the discovery of biomarkers. For example, the identification of proximal fluid and membrane proteins might help detect breast cancer. Another example would be the use of putative plasma protein biomarkers to identify acute-on-chronic liver failure (ACLF).


Traditional protein identification methods, such as immunoblotting, comigration analysis of known or unknown proteins, and chemical sequencing, are complex, time-consuming, and might be inaccurate. At ITSI-Biosciences, we offer a range of fast and accurate mass spectrometry services, including Forensic Mass Spectrometry Protein Analysis. Contact us today for more information!