Improved open modification searching in ANN-SoLo v0.4.0 - Further Analysis

This is the extra analysis of ANN-SoLo v0.4.0. ANN-SoLo spectral library search engine is a tool for efficient open modification searching. ANN-SoLo uses a cascade search strategy to optimally identify both unmodified and modified peptides: in the first stage a standard search is performed to identify unmodified peptides, after which the remaining unidentified spectra are submitted to second stage during which an open search is performed to additionally identify modified peptides. We have enhanced the software by integrating with Prosit to generate predicted spectral libraries from protein sequence databases, expanding support for a wider range of input library and query file formats, handling decoy generation internally, introducing an optimized internal file structure designed for large-scale analytics, and improving search accuracy by incorporating complementary ion information into vector-based spectral representations. To evaluate the effect of the enhancements implemented in ANN-SoLo version 0.4.0 and in addtion to this analysis, we performed extra analyses on three benchmark datasets as follows: CI_Analysis: This analysis focuses on the complementary ion-aware vectorization enhancement, demonstrating that the new version of the software achieves more accurate identifications while using fewer nearest-neighbor candidates. (Dataset: iPRG2012) Gl_Proteomics_data_Analysis: This analysis examines four query files from the human glycoproteomics dataset using two different search strategies: one with a decoy spectral library generated internally by the software, and another using a decoy library generated by SpectraST. The results show that both approaches yield comparable search outcomes. (Dataset: PXD009476) Ph_Proteomics_Data_Analysis: This analysis evaluates four query files from the HeLa phosphoproteomics dataset, again using the two search strategies described above. The findings indicate that the internally generated decoy library produces results comparable to those obtained with the SpectraST-generated library. (Dataset: PXD004452)