title: Processing strategies and software solutions for data-independent acquisition in mass spectrometry.
abstract: Data-independent acquisition (DIA) offers several advantages over data-dependent acquisition (DDA) schemes for characterizing complex protein digests analyzed by LC-MS/MS. In contrast to the sequential detection, selection, and analysis of individual ions during DDA, DIA systematically parallelizes the fragmentation of all detectable ions within a wide m/z range regardless of intensity, thereby providing broader dynamic range of detected signals, improved reproducibility for identification, better sensitivity, and accuracy for quantification, and, potentially, enhanced proteome coverage. To fully exploit these advantages, composite or multiplexed fragment ion spectra generated by DIA require more elaborate processing algorithms compared to DDA. This review examines different DIA schemes and, in particular, discusses the concepts applied to and related to data processing. Available software implementations for identification and quantification are presented as comprehensively as possible and examples of software usage are cited. Processing workflows, including complete proprietary frameworks or combinations of modules from different open source data processing packages are described and compared in terms of software availability and usability, programming language, operating system support, input/output data formats, as well as the main principles employed in the algorithms used for identification and quantification. This comparative study concludes with further discussion of current limitations and expectable improvements in the short- and midterm future.
authors.affiliation: Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland; Life Sciences Mass Spectrometry, School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Geneva, Switzerland.
authors.forename: Aivett
authors.initials: A
authors.lastname: Bilbao
authors.forename: Emmanuel
authors.initials: E
authors.lastname: Varesio
authors.forename: Jeremy
authors.initials: J
authors.lastname: Luban
authors.forename: Caterina
authors.initials: C
authors.lastname: Strambio-De-Castillia
authors.forename: Gérard
authors.initials: G
authors.lastname: Hopfgartner
authors.forename: Markus
authors.initials: M
authors.lastname: Müller
authors.forename: Frédérique
authors.initials: F
authors.lastname: Lisacek
mesh_terms: D002853:Chromatography, Liquid / Q000379:methods*; D013058:Mass Spectrometry / Q000379:methods*; D040901:Proteomics / Q000379:methods*; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D012984:Software
keywords: Bottom-up proteomics; Data processing and analysis; Data-independent acquisition; Label-free quantification; Mass spectrometry-LC-MS/MS