Intermittent fasting
(IF) increases lifespan and decreases metabolic
disease phenotypes and cancer risk in model organisms, but the health
benefits of IF in humans are less clear. Human plasma derived from
clinical trials is one of the most difficult sample sets to analyze
using mass spectrometry-based proteomics due to the extensive sample
preparation required and the need to process many samples to achieve
statistical significance. Here, we describe an optimized and accessible
device (Spin96) to accommodate up to 96 StageTips, a widely used sample
preparation medium enabling efficient and consistent processing of
samples prior to LC–MS/MS. We have applied this device to the
analysis of human plasma from a clinical trial of IF. In this longitudinal
study employing 8-weeks IF, we identified significant abundance differences
induced by the IF intervention, including increased apolipoprotein
A4 (APOA4) and decreased apolipoprotein C2 (APOC2) and C3 (APOC3).
These changes correlated with a significant decrease in plasma triglycerides
after the IF intervention. Given that these proteins have a role in
regulating apolipoprotein particle metabolism, we propose that IF
had a positive effect on lipid metabolism through modulation of HDL
particle size and function. In addition, we applied a novel human
protein variant database to detect common protein variants across
the participants. We show that consistent detection of clinically
relevant peptides derived from both alleles of many proteins is possible,
including some that are associated with human metabolic phenotypes.
Together, these findings illustrate the power of accessible workflows
for proteomics analysis of clinical samples to yield significant biological
insight.