ICan: an optimized ion-current-based quantification procedure with enhanced quantitative accuracy and sensitivity in...

Area of Science:

• Proteomics
• Analytical Chemistry
• Biotechnology

Background:

• High-resolution mass spectrometry enables advanced ion-current-based relative quantification.
• Current methods face challenges in quantitative sensitivity, accuracy, and false discovery rates.
• There is a need for improved data analysis procedures in quantitative proteomics.

Purpose of the Study:

• To introduce ICan, an integrated procedure for data normalization and protein ratio estimation.
• To enhance the accuracy, precision, and reduce false discovery rates in ion-current-based mass spectrometry analysis.
• To evaluate ICan's performance in detecting small fold-change proteins using a spiked-in experiment.

Main Methods:

• Development of the ICan procedure for normalization and protein ratio estimation.
• Application of ICan to high-resolution mass spectrometry data.
• Validation using a spiked-in experiment with E. coli extracts and human plasma proteins at a 1.5-fold change level.

Main Results:

• ICan demonstrated significantly improved accuracy, precision, and a lower false-positive rate compared to existing pipelines.
• In a spiked-in experiment, ICan correctly identified 92% of low-abundance proteins with a 1.5-fold change.
• No false positives were detected among reference proteins, highlighting ICan's specificity.

Conclusions:

• ICan offers a robust and sensitive approach for proteomic surveys using high-resolution mass spectrometry.
• The method is effective in reliably detecting small quantitative changes in proteins.
• ICan's features are valuable for both ion-current-based and isotope-labeling quantitative proteomics.