Targeted Proteomics: Benefits and Techniques

NewsGuard 100/100 Score

An emerging area in the field of proteomics is targeted proteomics, a technique concerned with the quantification of specific proteins. This method has high accuracy, reproducibility, and multiplexing capabilities.

Targeted proteomics is a technique concerned with the quantification of specific proteinspetarg | Shutterstock

What is proteome?

The proteome of the cell genome is more insightful compared to its transcriptome as proteins directly determine and alter cellular function. Post‐translational modification of existing proteins, increased abundance or allosterically modulated protein conformations have been tied to complex diseases, including Alzheimer’s, cancer, and diabetes. Existing methods of quantifying these changes have limitations due to a lack of specificity and variation in the procedure. Targeted proteomics presents a method to overcome these drawbacks.

Designing and performing targeted proteomics

Shotgun proteomics

Traditional methods to quantify protein interactions have used the shotgun proteomics approach, involving profiling the protein complement of numerous samples in an unbiased manner to compare the differential abundance of proteins. However, the exact shotgun method chosen depends on the data. Targeted proteomics is a refined approach to the shotgun or discovery method.

Another method used to quantify proteins is data‐independent acquisition (DIA). This method combines discovery proteomics with selected reaction monitoring (SRM). SRM is performed in a mass spectrometer which allows targeted measurement of a protein to occur as a selected peptide or fragment can be followed.

Tandem mass spectrometry (MS/MS) is the employed method of SRM. MS/MS separates proteins firstly by their mass-to-charge ratio, fragments the proteins and detects the resultant ions by a second mass spectrometer.

Bottom-up approach

In this method, initial measurements are acquired from a protein of interest which has been proteolytically cleaved into its constituent peptides. This yields a series of tryptic peptides which are then applied to a liquid chromatography (LC) column. Here, most proteins bind to the hydrophobic stationary phase (column). As the mobile phase becomes decreasingly polar, detachment and elution of the peptides occurs, providing the retention time for each peptide.

From this, the peptides are sequentially introduced into the mass spectrometer. Electron spray ionization (ESI) is used to ionize the peptides so that they carry a single positive charge and progress through the first quadrupole (Q1).

Fragmentation occurs through the process of collusion‐induced dissociation to produce a set of fragment ions at the second quadrupole (Q2). From these fragmented ions, a further selection event takes places at the third quadrupole (Q3) and subsequently detected by a mass analyzer.

Parallel reaction monitoring (PRM)

Parallel reaction monitoring (PRM) is another method that is performed on a high‐resolution hybrid instrument which allows all possible ions to be monitored by the mass analyzer. The area integrated under the fragment ion peaks is a measurement of the fragment ion abundance which can be used to determine the mass of the unique precursor ion, and subsequently, the protein.

The competitive edge of targeted proteomics

In the clinical setting, targeted proteomics allows the development of personalized medicine. For example, stratification of patients is possible with targeted proteomics as responders and non-responders can be grouped for treatment.

Additionally, a pre-defined set of biomarker protein panel can be developed for screening of diseases (including their stage) which facilitates early diagnosis and allows epidemic management within a population.

In order to make targeted proteomics an integral part of the research, it needs to be more accessible. Further, efforts are required to build the infrastructure to support data analysis, instrumentation, and expertise. Automation is desirable at all stages from sample processing, instrument handling, and data analysis.


  • Anjali Arora & Kumaravel Somasundaram. Targeted Proteomics Comes to the Benchside and the Bedside: Is it Ready for Us? Bioessays. 2019.
  • Eva Borràs & Eduard Sabidó. 2017. What is targeted proteomics? A concise revision of targeted acquisition and targeted data analysis in mass spectrometry. Proteomics.
  • Nagib Ahsanab, Shyama Prasad Raoc, Philip A.Gruppusode, Bharat Ramratnamab, Arthur R. Salomonbe. Targeted proteomics: Current status and future perspectives for quantification of food allergens. 2016. Journal of Proteomics. 143. pp.15-23.

Further Reading

Last Updated: Apr 24, 2019

Hidaya Aliouche

Written by

Hidaya Aliouche

Hidaya is a science communications enthusiast who has recently graduated and is embarking on a career in the science and medical copywriting. She has a B.Sc. in Biochemistry from The University of Manchester. She is passionate about writing and is particularly interested in microbiology, immunology, and biochemistry.


Please use one of the following formats to cite this article in your essay, paper or report:

  • APA

    Aliouche, Hidaya. (2019, April 24). Targeted Proteomics: Benefits and Techniques. News-Medical. Retrieved on May 24, 2024 from

  • MLA

    Aliouche, Hidaya. "Targeted Proteomics: Benefits and Techniques". News-Medical. 24 May 2024. <>.

  • Chicago

    Aliouche, Hidaya. "Targeted Proteomics: Benefits and Techniques". News-Medical. (accessed May 24, 2024).

  • Harvard

    Aliouche, Hidaya. 2019. Targeted Proteomics: Benefits and Techniques. News-Medical, viewed 24 May 2024,


The opinions expressed here are the views of the writer and do not necessarily reflect the views and opinions of News Medical.
Post a new comment

While we only use edited and approved content for Azthena answers, it may on occasions provide incorrect responses. Please confirm any data provided with the related suppliers or authors. We do not provide medical advice, if you search for medical information you must always consult a medical professional before acting on any information provided.

Your questions, but not your email details will be shared with OpenAI and retained for 30 days in accordance with their privacy principles.

Please do not ask questions that use sensitive or confidential information.

Read the full Terms & Conditions.

You might also like...
Study observes rapid immune response in individuals switching to vegan and keto diets