In
order for mass spectrometry to continue to grow as
a platform
for high-throughput clinical and translational research, careful consideration
must be given to quality control by ensuring that the assay performs
reproducibly and accurately and precisely. In particular, the throughput
required for large cohort clinical validation in biomarker discovery
and diagnostic screening has driven the growth of multiplexed targeted
liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS)
assays paired with sample preparation and analysis in multiwell plates.
However, large scale MS-based proteomics studies are often plagued
by batch effects: sources of technical variation in the data, which
can arise from a diverse array of sources such as sample preparation
batches, different reagent lots, or indeed MS signal drift. These
batch effects can confound the detection of true signal differences,
resulting in incorrect conclusions being drawn about significant biological
effects or lack thereof. Here, we present an intraplate batch effect
termed the edge effect arising from temperature gradients in multiwell
plates, commonly reported in preclinical cell culture studies but
not yet reported in a clinical proteomics setting. We present methods
herein to ameliorate the phenomenon including proper assessment of
heating techniques for multiwell plates and incorporation of surrogate
standards, which can normalize for intraplate variation.