Epsilon-Q: An Automated Analyzer Interface for Mass Spectral Library Search and Label-Free Protein Quantification

Mass spectrometry (MS) is a widely
used proteome analysis tool
for biomedical science. In an MS-based bottom-up proteomic approach
to protein identification, sequence database (DB) searching has been
routinely used because of its simplicity and convenience. However,
searching a sequence DB with multiple variable modification options
can increase processing time, false-positive errors in large and complicated
MS data sets. Spectral library searching is an alternative solution,
avoiding the limitations of sequence DB searching and allowing the
detection of more peptides with high sensitivity. Unfortunately, this
technique has less proteome coverage, resulting in limitations in
the detection of novel and whole peptide sequences in biological samples.
To solve these problems, we previously developed the “Combo-Spec
Search” method, which uses manually multiple references and
simulated spectral library searching to analyze whole proteomes in
a biological sample. In this study, we have developed a new analytical
interface tool called “Epsilon-Q” to enhance the functions
of both the Combo-Spec Search method and label-free protein quantification.
Epsilon-Q performs automatically multiple spectral library searching,
class-specific false-discovery rate control, and result integration.
It has a user-friendly graphical interface and demonstrates good performance
in identifying and quantifying proteins by supporting standard MS
data formats and spectrum-to-spectrum matching powered by SpectraST.
Furthermore, when the Epsilon-Q interface is combined with the Combo-Spec
search method, called the Epsilon-Q system, it shows a synergistic
function by outperforming other sequence DB search engines for identifying
and quantifying low-abundance proteins in biological samples. The
Epsilon-Q system can be a versatile tool for comparative proteome
analysis based on multiple spectral libraries and label-free quantification.