Spectral library search for improved TMTpro labelled peptide assignment in human plasma proteomics

Area of Science:

• Proteomics
• Biomarker Discovery
• Mass Spectrometry

Background:

• Human plasma proteomics is crucial for clinical biomarker discovery.
• High dynamic range and complexity of plasma challenge mass spectrometry-based identification.
• Current methods require extensive pre-analytical sample preparation.

Purpose of the Study:

• To develop and evaluate a TMTpro-specific spectral library for improved human plasma proteomics.
• To enhance protein identification without additional pre-analytical sample preparation.
• To provide a resource for future plasma proteomics research.

Main Methods:

• Constructed a spectral library using LC-MS/MS analysis of fractionated TMTpro-tagged human plasma, cell lysates, and arterial tissues.
• Curated the library with quality filters for reliable peptide identifications.
• Compared spectral library searching against conventional sequence database searching.

Main Results:

• Spectral library searching significantly improved protein identification in plasma samples.
• Identifications showed high complementarity with sequence database search results.
• Demonstrated increased protein identifications without extra sample preparation.

Conclusions:

• A TMTpro-specific spectral library effectively enhances human plasma proteomics.
• This approach increases protein identification accuracy and speed.
• The publicly available library (PXD042546) supports future research and algorithm optimization.