CsoDIAq Software for Direct Infusion Shotgun Proteome Analysis

New mass spectrometry data collection methods require new computational tools. 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 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 (MaCC), which improves target discrimination in a target-decoy analysis. We further show that reanalysis after fragment mass tolerance correction 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.