title: Optimization of Acquisition and Data-Processing Parameters for Improved Proteomic Quantification by Sequential Window Acquisition of All Theoretical Fragment Ion Mass Spectrometry.
abstract: Proteomic analysis with data-independent acquisition (DIA) approaches represented by the sequential window acquisition of all theoretical fragment ion spectra (SWATH) technique has gained intense interest in recent years because DIA is able to overcome the intrinsic weakness of conventional data-dependent acquisition (DDA) methods and afford higher throughout and reproducibility for proteome-wide quantification. Although the raw mass spectrometry (MS) data quality and the data-mining workflow conceivably influence the throughput, accuracy and consistency of SWATH-based proteomic quantification, there lacks a systematic evaluation and optimization of the acquisition and data-processing parameters for SWATH MS analysis. Herein, we evaluated the impact of major acquisition parameters such as the precursor mass range, isolation window width and accumulation time as well as the data-processing variables including peak extraction criteria and spectra library selection on SWATH performance. Fine tuning these interdependent parameters can further improve the throughput and accuracy of SWATH quantification compared to the original setting adopted in most SWATH proteomic studies. Furthermore, we compared the effectiveness of two widely used peak extraction software PeakView and Spectronaut in discovery of differentially expressed proteins in a biological context. Our work is believed to contribute to a deeper understanding of the critical factors in SWATH MS experiments and help researchers optimize their SWATH parameters and workflows depending on the sample type, available instrument and software.
authors.affiliation: iHuman Institute, ShanghaiTech University , Shanghai 201210, China.
authors.forename: Shanshan
authors.initials: S
authors.lastname: Li
authors.affiliation: Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences , Tianjin 300308, China.
authors.forename: Qichen
authors.initials: Q
authors.lastname: Cao
authors.affiliation: College of Life Sciences, Nankai University , Tianjin 300071, China.
authors.forename: Weidi
authors.initials: W
authors.lastname: Xiao
authors.affiliation: Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences , Tianjin 300308, China.
authors.forename: Yufeng
authors.initials: Y
authors.lastname: Guo
authors.affiliation: College of Life Sciences, Nankai University , Tianjin 300071, China.
authors.forename: Yunfei
authors.initials: Y
authors.lastname: Yang
authors.affiliation: College of Life Sciences, Nankai University , Tianjin 300071, China.
authors.forename: Xiaoxiao
authors.initials: X
authors.lastname: Duan
authors.affiliation: iHuman Institute, ShanghaiTech University , Shanghai 201210, China.
authors.forename: Wenqing
authors.identifier: 0000-0002-5245-2477
authors.initials: W
authors.lastname: Shui
mesh_terms: D002853:Chromatography, Liquid / Q000706:statistics & numerical data; D057225:Data Mining; D011499:Protein Processing, Post-Translational / Q000235:genetics*; D020543:Proteome / Q000235:genetics*; D040901:Proteomics / Q000706:statistics & numerical data*; D012984:Software; D053719:Tandem Mass Spectrometry / Q000379:methods
chemical_list: D020543:Proteome
keywords: DIA; SWATH; acquisition parameters; data processing; proteomic quantification; spectral library