A proteomics performance standard to support measurement quality in proteomics

Area of Science:

• Biochemistry
• Biomedical Research
• Proteomics

Background:

• Mass spectrometry (MS)-based proteomic platforms are crucial in biochemical and biomedical research.
• The increasing use of these platforms necessitates high-quality MS measurements for reliable results.
• Existing quality control materials may not fully address the complexities of proteomics workflows.

Purpose of the Study:

• To introduce NIST reference material (RM) 8323, a yeast protein extract, as a quality control material for proteomics.
• To enable benchmarking of preanalytical and analytical performance in proteomics workflows.
• To support the design and optimization of proteomics methodologies from sample preparation to data analysis.

Main Methods:

• Utilized NIST RM 8323, a well-characterized Saccharomyces cerevisiae protein extract.
• Coupled liquid chromatography-tandem mass spectrometry (LC-MS/MS) with NIST MS Quality Control (MSQC) performance metrics.
• Applied these methods to quantitatively assess LC-MS/MS instrumentation parameters and sample preparation techniques.

Main Results:

• Demonstrated the utility of RM 8323 and MSQC metrics for assessing LC-MS/MS instrumentation performance.
• Quantitatively evaluated parameters influencing measurement accuracy, repeatability, and reproducibility.
• Showcased the application of RM 8323 and MSQC metrics in optimizing proteomics sample preparation methods for complex proteomes.

Conclusions:

• NIST RM 8323 serves as a valuable proteomics quality control material.
• The combination of RM 8323 and MSQC metrics effectively benchmarks proteomics workflows.
• This approach aids in improving the reliability and reproducibility of MS-based proteomics research.