SILVER

SILVER quantifies stable isotope labeling mass spectrometry (MS) data for quantitative proteomics by providing spectrum-, peptide-, and protein-level measurement with integrated quality control.

Key Features:

• Novel quality control methods: Implements multi-tiered QC at the spectrum, peptide, and protein levels to validate quantification results.
• Quantification confidence filters and indices: Employs multiple confidence filters and indices tailored to refine accuracy of stable isotope-labeling quantification.
• Performance verification: Benchmarked against MaxQuant and Proteome Discoverer using large-scale and standard datasets, demonstrating high accuracy, robustness, and significantly reduced processing time.

Scientific Applications:

• Quantitative proteomics: Provides precise measurement of protein abundance using stable isotope labeling MS.
• Biomarker discovery: Supports identification of differential protein abundance for biomarker studies.
• Pathway analysis: Enables comparative quantification for pathway-level investigations.
• Comparative proteomic studies: Facilitates condition-to-condition comparisons using stable isotope labeling approaches.

Methodology:

Implements spectrum-, peptide-, and protein-level QC methods and quantification confidence filters/indices, and was benchmarked against MaxQuant and Proteome Discoverer on large-scale and standard datasets with measurement of processing time.