Isobaric labeling is a powerful strategy for quantitative mass
spectrometry-based proteomic investigations. A complication of such analyses has
been the co-isolation of multiple analytes of similar mass-to-charge resulting
in the distortion of relative protein abundance measurements across samples.
When properly implemented, triple-stage mass spectrometry and synchronous
precursor selection (SPS-MS3) can reduce the occurrence of this phenomena,
referred to as ion interference. However, no diagnostic tool is available
currently to rapidly and accurately assess ion interference. To address this
need, we developed a multiplexed TMT-based standard, termed the triple knockout
(TKO). This standard is comprised of three yeast proteomes in triplicate, each
from a strain deficient in a highly abundant protein (Met6, Pfk2, or Ura2). The
relative abundance patterns of these proteins, which can be inferred from dozens
of peptide measurements, are representative of ion interference in peptide
quantification. We expect no signal in channels where the protein is knocked
out, permitting maximum sensitivity for measurements of ion interference against
a null background. Here, we emphasize the need to investigate further ion
interference-generated ratio distortion and promote the TKO standard as a tool
to investigate such issues.