Matrix-Matched Calibration Curves for Assessing Analytical Figures of Merit in Quantitative Proteomics
Lindsay K. Pino, Brian C. Searle, Han-Yin Yang, Andrew N. Hoofnagle, William Stafford Noble, Michael J. MacCoss
Abstract
Mass spectrometry is a powerful tool for quantifying protein abundance in complex samples. Advances in sample preparation and the development of data-independent acquisition (DIA) mass spectrometry approaches have increased the number of peptides and proteins measured per sample. Here, we present a series of experiments demonstrating how to assess whether a peptide measurement is quantitative by mass spectrometry. Our results demonstrate that increasing the number of detected peptides in a proteomics experiment does not necessarily result in increased numbers of peptides that can be measured quantitatively.
Topics & Concepts
Quantitative proteomicsMass spectrometryProteomicsChromatographyCalibrationCalibration curveMatrix (chemical analysis)Quantitative analysis (chemistry)PeptideLabel-free quantificationSample (material)ChemistryIsobaric labelingAnalytical Chemistry (journal)Tandem mass spectrometryProtein mass spectrometryMathematicsStatisticsBiochemistryDetection limitGeneAdvanced Proteomics Techniques and ApplicationsMass Spectrometry Techniques and ApplicationsMetabolomics and Mass Spectrometry Studies