DIALib-QC an assessment tool for spectral libraries in data-independent acquisition proteomics

• Published in: Nature communications Vol. 11; no. 1; p. 5251
• Main Authors: Midha, Mukul K., Campbell, David S., Kapil, Charu, Kusebauch, Ulrike, Hoopmann, Michael R., Bader, Samuel L., Moritz, Robert L.
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 16-10-2020; Nature Publishing Group; Nature Portfolio
• Subjects: 631/114/2784; 631/45/475; 82/58; 82/75; 82/81; Evaluation; Humanities and Social Sciences; Humans; Libraries; Mass spectra; Mass spectrometry; Mass Spectrometry - methods; Mass Spectrometry - standards; Mass spectroscopy; multidisciplinary; Peptide Library; Peptides; Peptides - chemistry; Peptides - genetics; Proteins - chemistry; Proteins - genetics; Proteomics; Proteomics - methods; Proteomics - standards; Quality assessment; Quality control; Science; Science (multidisciplinary); Software; Software development tools
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-020-18901-y

Data-independent acquisition (DIA) mass spectrometry, also known as Sequential Window Acquisition of all Theoretical Mass Spectra (SWATH), is a popular label-free proteomics strategy to comprehensively quantify peptides/proteins utilizing mass spectral libraries to decipher inherently multiplexed spectra collected linearly across a mass range. Although there are many spectral libraries produced worldwide, the quality control of these libraries is lacking. We present the DIALib-QC (DIA library quality control) software tool for the systematic evaluation of a library’s characteristics, completeness and correctness across 62 parameters of compliance, and further provide the option to improve its quality. We demonstrate its utility in assessing and repairing spectral libraries for correctness, accuracy and sensitivity.
Most data-independent acquisition (DIA) methods depend on mass spectral libraries for peptide identification but tools to assess library quality are lacking. Here, the authors develop DIALib- QC for the systematic evaluation and correction of spectral libraries.