Longitudinal Large-Scale Semiquantitative Proteomic Data Stability Across Multiple Instrument Platforms

• DOI: 10.1021/acs.jproteome.1c00624
• Publication Date: 2021-10-21T00:54:20Z
• Authors: Congcong Lu; Tina Glisovic-Aplenc; Kathrin M. Bernt; Kevin Nestler; Joseph Cesare; Lusha Cao; Hyoungjoo Lee; Hossein Fazelinia; Asif Chinwalla; Yang Xu; Olga Shestova; Yi Xing; Saar Gill; Mingyao Li; Benjamin Garcia; Richard Aplenc
• Keywords: Orbitrap; Proteome; Biomarker Discovery

With the rapid developments in mass spectrometry (MS)-based proteomics methods, label-free semiquantitative has become an increasingly popular tool for profiling global protein abundances unbiased manner. However, reproducibility of these data across time and LC–MS platforms is not well characterized. Here, we evaluate performance three (Orbitrap Elite, Q Exactive HF, Orbitrap Fusion) analysis cell surface proteins over a six-year period. Sucrose gradient ultracentrifugation was used surfaceome enrichment, following gel separation in-depth identification. our established workflow, consistently detected reproducibly quantified >2300 putative human acute myeloid leukemia (AML) line on all platforms. To knowledge this first study reporting highly reproducible proteomic collection biological replicates multiple years These provide experimental justification designs that are executed multiyear intervals different Multiyear multiplatform will likely enable larger scale studies facilitate longitudinal by investigators lacking access to high throughput MS facilities. Data available via ProteomeXchange with identifier PXD022721.