Pseudo isobaric peptide termini labelling for relative proteome quantification by SWATH MS acquisition

Area of Science:

• Proteomics
• Mass Spectrometry
• Quantitative Biology

Background:

• Pseudo isobaric peptide termini labeling (IPTL) offers high quantitative accuracy in proteomics.
• Limitations of DDA-pseudo-IPTL include irreproducible precursor ion selection and chromatographic shifts.

Purpose of the Study:

• To develop a novel quantitative proteomics strategy by expanding pseudo IPTL to SWATH MS.
• To improve the accuracy and precision of quantitative proteomics compared to DDA-based methods.

Main Methods:

• Developed SWATH-pseudo-IPTL by integrating pseudo IPTL with SWATH MS.
• Utilized complete extracted ion chromatogram (XIC) intensity of MS/MS scans for quantification.
• Validated the method using mixed HeLa samples and applied it to hepatocellular carcinoma cell lines.

Main Results:

• SWATH-pseudo-IPTL demonstrated superior accuracy and precision compared to DDA-pseudo-IPTL.
• Quantitative profiling of hepatocellular carcinoma cell lines identified proteins related to tumorigenesis and metastasis.

Conclusions:

• SWATH-pseudo-IPTL is a robust and accurate quantitative proteomics strategy.
• The method is feasible for biological applications, including cancer research.