SpecQuality: A Tool for Reliable Spectral Quality Assessment in Proteomics and Proteogenomics

Proteogenomics integrates genomics and mass spectrometry (MS) data to understand complex biological systems, disease mechanisms, and potential biomarkers. However, the high volume and noise in MS data present computational and interpretational challenges in proteogenomic studies where, despite best efforts, many spectra are often left unassigned. We developed <i>SpecQuality</i>, an easy-to-use tool for MS/MS quality assessment. We evaluated ten spectral features and, using the top features, developed a machine learning-based model to predict the quality of MS/MS spectra through a spectral quality score (SQS). SpecQuality can be used prior to database search or for postsearch validation of peptide spectrum matches (PSMs). This enables rapid prioritization of high-quality PSMs from proteomics and proteogenomics searches, thereby reducing false-positive identifications. We demonstrated its utility in proteogenomics applications by evaluating its performance on two data sets with ∼2.7 million spectra from Alzheimer's disease, where it successfully highlighted high quality spectra. The spectra that matched novel, variant, and modified peptides in the proteogenomics search were observed to be of high spectral quality. Additionally, a direct comparison with manually curated variant identifications demonstrated its capacity to mitigate false positives and enhance reliability. SpecQuality is an open-source, freely available, easy-to-use, simple, and versatile tool developed in both Python and Perl that can be leveraged in many proteomics pipelines. It can be easily used as a standalone tool or integrated as a part of a bioinformatics data analysis pipeline. SpecQuality provides a scalable and accessible approach to spectral prioritization, advancing data integrity in proteomics and proteogenomics. SpecQuality is available at https://github.com/alkayadav10/SpecQuality.