biostudies-literatureMcDonnell KIrish Research Council1402-1412https://www.ebi.ac.uk/biostudies/studies/S-EPMC8956878biostudies-literatureUnknown20Proteomics aims to characterise system-wide protein expression and typically relies on mass-spectrometry and peptide fragmentation, followed by a database search for protein identification. It has wide ranging applications from clinical to environmental settings and virtually impacts on every area of biology. In that context, <i>de novo</i> peptide sequencing is becoming increasingly popular. Historically its performance lagged behind database search methods but with the integration of machine learning, this field of research is gaining momentum. To enable <i>de novo</i> peptide sequencing to realise its full potential, it is critical to explore the mass spectrometry data underpinning peptide identification. In this research we investigate the characteristics of tandem mass spectra using 8Computational and structural biotechnology journalThe impact of noise and missing fragmentation cleavages on <i>de novo</i> peptide identification algorithms.PMC8956878GOIPG/2019/1650Abram FMcDonnell KHowley EfalseThe impact of noise and missing fragmentation cleavages on <i>de novo</i> peptide identification algorithms.Proteomics aims to characterise system-wide protein expression and typically relies on mass-spectrometry and peptide fragmentation, followed by a database search for protein identification. It has wide ranging applications from clinical to environmental settings and virtually impacts on every area of biology. In that context, <i>de novo</i> peptide sequencing is becoming increasingly popular. Historically its performance lagged behind database search methods but with the integration of machine learning, this field of research is gaining momentum. To enable <i>de novo</i> peptide sequencing to realise its full potential, it is critical to explore the mass spectrometry data underpinning peptide identification. In this research we investigate the characteristics of tandem mass spectra using 82022-01-01T00:00:00Z20222026-05-31T07:13:48.245Z2024-11-21T02:47:45.937ZS-EPMC89568783538610410.1016/j.csbj.2022.03.008