A new SWATH ion library for mouse adult hippocampal neural stem cells

TL;DR

This paper presents a newly created SWATH ion library specifically for mouse adult hippocampal neural stem cells, facilitating proteomics research in neuroscience by simplifying data analysis.

Contribution

The authors provide a tailored SWATH ion library for mouse hippocampal neural stem cells, reducing the effort needed to build such libraries for proteomics studies.

Findings

Enables easier and faster proteomics analysis in neuroscience.

Supports high-throughput and accurate quantification of proteins.

Facilitates research on neural stem cells in mice.

Abstract

Over the last years, the SWATH data-independent acquisition protocol (Sequential Window acquisition of All THeoretical mass spectra) has become a cornerstone for the worldwide proteomics community. In this approach, a high-resolution quadrupole-ToF mass spectrometer acquires thousands of MS/MS data by selecting not just a single precursor at a time, but by allowing a broad m/z range to be fragmented. This acquisition window is then sequentially moved from the lowest to the highest mass selection range. This technique enables the acquisition of thousands of high-resolution MS/MS spectra per minute in a standard LC-MS run. In the subsequent data analysis phase, the corresponding dataset is searched in a triple quadrupole-like mode, thus not considering the whole MS/MS scan spectrum, but by searching for several precursor to fragment transitions that identify and quantify the corresponding peptide. This search is made possible with the use of an ion library, previously acquired in a classical data dependent, full-spectrum mode. The SWATH protocol, combining the protein identification power of high-resolution MS/MS spectra with the robustness and accuracy in analyte quantification of triple-quad targeted workflows, has become very popular in proteomics research. The major drawback lies in the ion library itself, which is normally demanding and time-consuming to build. Conversely, through the realignment of chromatographic retention times, an ion library of a given proteome can relatively easily be tailored upon any proteomics experiment done on the same proteome. We are thus hereby sharing with the worldwide proteomics community our newly acquired ion library of mouse adult hippocampal neural stem cells. Given the growing effort in neuroscience research involving proteomics experiments, we believe that this data might be of great help for the neuroscience community.