Each experiment directory contains the Thermo RAW files for all the matched matrix calibration curves (yeast_curves, csf_curves, and ffpe_curves; water_curves and hela_curves refer to the yeast reference proteome diluted in water and hela backgrounds, respectively). The folder "demultiplexed_mzml" contains the demultiplexed converted files used as input for the Skyline documents and for the EncyclopeDIA analyses. For the EncyclopeDIA outputs, please see the "Data Matrices" tab (top right).

The outputs from EncyclopeDIA analyses are stored here. To view ELIB files, we recommend DB Browser for SQL Lite. The *elib.peptides.txt files (can be viewed in the browser under the Lists tab or downloaded from the EncyclopeDIA Outputs tab) were used as the quantitative matrix inputs for the calibration curves in the manuscript.

In this project, we propose a framework for discriminating between detected and quantitative peptides in proteomics experiments. We introduce an alternative to stable isotope label calibration curves called "matched matrix calibration curves, and we demonstrate the method using yeast as a model system. We additionally apply the proposed framework for cerebrospinal fluid (CSF) proteomics and formalin-fixed paraffin-embedded (FFPE) renal biopsies. We find that, regardless of the sample type, the framework shows that not all detected peptides are quantitative, and that peptide LOQs range orders of magnitude even within the same protein. This illustrates the need for additional criteria to ensure that detected peptides are also quantitative. We thus demonstrate that proteomics experiments employing matched matrix calibration curves can produce truly quantitative measurements of peptides and proteins at the scale of an entire proteome.