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

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