We have developed MetaboKit, a comprehensive software package for compound identification and relative quantification in mass spectrometry-based untargeted metabolomics analysis.

Data-independent acquisition (DIA) approaches, such as SWATH -MS, are showing great potential to reliably quantify significant numbers of peptides and proteins in an unbiased manner. These developments have enhanced interest in developing a single DIA method which integrates qualitative and quantitative analysis, eliminating the need of a pre-built library of peptide spectra which are created through data-dependent acquisition (DDA) methods or from public repositories. Here we introduce a new DIA approach, referred to as "SWATH-ID", which was developed to allow peptide identification as well as quantitation. The SWATH-ID method is composed of small Q1 windows, achieving better selectivity and thus significantly improving high-confidence peptide extractions from data files. Furthermore, the SWATH-ID approach transmits precursor ions without fragmentation as well as their fragments within the same SWATH acquisition period. This provides a single scan which includes all precursor ions within the isolation window as well as a record of all of their fragment ions, substantially negating the need for a survey scan. In this way all precursors present in a small Q1 window are associated with their fragment ions, improving the identification specificity and providing a more comprehensive and in-depth view of protein and peptide species in complex samples. This article is protected by copyright. All rights reserved.

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