Oral Presentation HUPO 2019 - 18th Human Proteome Organization World Congress

Standardizing the performance of SWATH/DIA-MS software tools for label-free quantification using public repository spectral ion libraries (#219)

Robert Moritz 1
  1. Institute For Systems Biology, Seattle, WA, United States

Spectral ion libraries are routinely used to analyze data derived from SWATH/DIA type mass spectrometry acquisition methods. For confidence in protein identification and quantitation using SWATH/DIA data, the characteristics of reference ion library is important when processing SWATH/DIA data for quantitative results. Different library construction methods can affect the performance of SWATH/DIA analysis that incorporate the expected multitude of non-standardized SWATH/DIA data acquisition method components such as chromatography flow rates, different mass spectrometry instruments, spectral quality and transferability, and SWATH/DIA analysis software tools. For a consistent assessment of reference ion libraries for SWATH/DIA analysis, we developed DIA-Lib QC, a library assessment tool built into the SWATHAtlas website (www.swathatlas.org) to calculate the metrics of library correctness and its completeness, which provides some level of interrogation for confidence in the database used for library-based SWATH/DIA analysis. With our benchmarking studies using hybrid ground-truth datasets, we evaluated the characteristics and performance of different SWATH/DIA-MS tools based on accuracy of identification, the precision of quantitation, quantitative sensitivity, and relative performance of these applications. Our analysis highlights many inconsistencies in available libraries and their performance for reliable quantification performance, and robustness in label-free quantitative proteomics.