MSstatsLOBD

MSstatsLOBD calculates and visualizes the limit of blank (LOB) and limit of detection (LOD) for peptide concentration measurements in mass spectrometry-based proteomics.

Key Features:

• LOB Calculation: Computes the highest apparent concentration of a peptide expected when replicates of a blank sample containing no peptides are measured.
• LOD Calculation: Computes the measured concentration value for which the probability of falsely claiming the absence of a peptide in the sample is 0.05, given a probability 0.05 of falsely claiming its presence.
• Visualization: Provides visualization capabilities for the calculated LOB and LOD values.

Scientific Applications:

• Assay Characterization: Supports characterization of mass spectrometry-based proteomic assays by establishing statistical limits for peptide detection.
• Peptide Quantification Validation: Enables determination of reliable detection thresholds for peptide concentration measurements in blank samples and low-abundance samples.

Methodology:

The methodology is described in Galitzine (2018) doi:10.1074/mcp.RA117.000322.