Final answer:
Protein iBAQ abundance values in SWATH mass spectrometry represent the relative abundance of proteins in a sample, calculated using the intensity of peptides. SIEVE is a commonly used quantification package for analyzing protein abundance in SWATH mass spectrometry.
Step-by-step explanation:
In SWATH mass spectrometry, protein iBAQ (intensity-based absolute quantification) abundance values are a measure of the relative abundance of proteins in a sample. These values are calculated using the intensity of peptides derived from proteins in the mass spectrometry data.
SIEVE, a label-free quantification package, is often used for the analysis of protein abundance in SWATH mass spectrometry. It compares the relative abundance of peptides and proteins in different groups (e.g., control vs. experimental) to identify significant differences in protein quantities.
Protein iBAQ abundance values are important for understanding changes in protein expression and identifying proteins that may play a role in biological processes or diseases.