Figure 1: Workflows for data acquisition, analysis, and dissemination.

(a) Flowchart of data acquisition, from in vivo labeling to the acquisition of Orbitrap mass spectrometry (MS) data. Normal and hypertrophic animals from A/J, BALB/cJ, C57BL/6J, CE/J, DBA/2J, and FVB/NJ mice were labeled for up to 14 days with ²H₂O. A total of 78 sample groups were analyzed independently at 7 time points. From each group, hearts were excised and subjected to subcellular fractionation. Proteins were extracted for trypsin digestion and analyzed by high-resolution Orbitrap MS to measure isotope incorporation. (b) Flowchart of data analysis strategy, from MS data to technical validation. Raw mass spectra and protein identification results were analyzed by ProTurn. The intensity and isotope profiles of peptide mass spectra were quantified by integration over chromatographic spaces, then tabulated into time series and fitted to kinetic curves to deduce turnover rates, followed by stringency filters. (c) Data dissemination strategy, encompassing raw data storage and collaborative analysis platform. I. Raw data are deposited to a raw data repository for proteomics data, ProteomeXchange, where data users can download stored MS files to support raw data re-analysis and method development (see use cases 3 and 4 in text). II. The processed data and turnover rate tables are disseminated on an open data analysis platform, Synapse, where users can look up protein turnover rates and compare cellular pathways (see use cases 1 and 2 in text).