CsoDIAq Software for Direct Infusion Shotgun Proteome Analysis

Direct infusion shotgun
proteome analysis (DISPA) is a new paradigm
for expedited mass spectrometry-based proteomics, but the original
data analysis workflow was onerous. Here, we introduce CsoDIAq, a
user-friendly software package for the identification and quantification
of peptides and proteins from DISPA data. In addition to establishing
a complete and automated analysis workflow with a graphical user interface,
CsoDIAq introduces algorithmic concepts to spectrum-spectrum matching
to improve peptide identification speed and sensitivity. These include
spectra pooling to reduce search time complexity and a new spectrum–spectrum
match score called match count and cosine, which improves target discrimination
in a target-decoy analysis. Fragment mass tolerance correction also
increased the number of peptide identifications. Finally, we adapt
CsoDIAq to standard LC–MS DIA and show that it outperforms
other spectrum–spectrum matching software.