Quantification of 782 Plasma Peptides by Multiplexed Targeted Proteomics

Area of Science:

• Clinical proteomics
• Mass spectrometry-based diagnostics
• Biomarker discovery

Background:

• Blood analysis is crucial for clinical diagnostics.
• Mass spectrometry has advanced protein identification and quantification in blood.
• Ion mobility enhances proteome coverage and reduces analysis time in mass spectrometry.

Purpose of the Study:

• To evaluate parallel reaction monitoring with parallel accumulation and serial fragmentation (PRM-PASEF) for plasma protein quantification.
• To introduce and assess guided data independent acquisition with parallel accumulation and serial fragmentation (g-DIA-PASEF) as a faster alternative.
• To demonstrate the utility of these methods for biomarker discovery in colorectal cancer (CRC) patient plasma.

Main Methods:

• Utilized PRM-PASEF with isotope-labeled peptides to quantify proteins in spiked plasma samples.
• Developed and applied g-DIA-PASEF for blood plasma analysis.
• Analyzed plasma samples from 20 colorectal cancer patients and controls using both methods.

Main Results:

• PRM-PASEF quantified 565 plasma proteins from a targeted peptide mix.
• g-DIA-PASEF demonstrated comparable performance to PRM-PASEF for plasma analysis.
• Identified 14 differentially regulated proteins between CRC patients and controls.

Conclusions:

• PRM-PASEF and g-DIA-PASEF are powerful targeted and untargeted proteomics techniques for blood plasma analysis.
• These methods enable rapid and unbiased screening for potential protein biomarkers.
• The techniques show promise for clinical diagnostics, including colorectal cancer biomarker discovery, without preselecting candidates.