Spectral Libraries for SWATH‐MS Assays for Drosophila melanogaster and Solanum lycopersicum

Abstract

Quantitative proteomics methods have emerged as powerful tools for measuring protein expression changes at the proteome level. Using mass-spectrometry (MS) based approaches, it is now possible to routinely quantify thousands of proteins. However, pre-fractionation of the samples at the protein or peptide level is usually necessary to go deep into the proteome, increasing both MS analysis time and technical variability. Recently, a new MS acquisition method named SWATH was introduced with the potential to provide good coverage of the proteome as well as a good measurement precision without prior sample fractionation. In contrast to shotgun based MS however, a library containing experimental acquired spectra is necessary for the bioinformatics analysis of SWATH data. In this study, we built spectral libraries for two widely used models to study crop ripening or animal embryogenesis, Solanum lycopersicum (tomato) and Drosophila melanogaster, respectively. The spectral libraries comprise fragments for 5,197 and 6,040 proteins for Solanum lycopersicum and Drosophila melanogaster, respectively, and allow reproducible quantification for thousands of peptides per MS analysis. The spectral libraries and all massspectrometry data are available in the MassIVE repository with the dataset identifiers MSV000081074 and MSV000081075 and the PRIDE repository with the dataset identifiers PXD006493 and PXD006495. For DIA, the spectral library contains experimental acquired spectra of the precursors and can be produced directly from the SWATH data, by reconstituting the MSMS spectra using the retention time of the precursors and the fragments [7], or by DDA analysis of the sample, which can be fractionated to increase the number of spectra in the library [9]. Ideally, the spectral library should be generated on a MS instrument similar to the one used to acquire further SWATH-MS data as the correlation of the fragment intensities for a peptide acquired on different instrument was shown to be rather low [10]. Although Rosenberger et al. recently published a library containing assays for 10,000 human proteins [9] and deep libraries for other applications such as SRM (Selected Reaction Monitoring) have been generated [11][12][13], the number of publicly available spectral libraries for SWATH-MS is still limited. Several other studies have produced libraries for other species [14][15][16]. However, spectral libraries are still missing for many species and, when available, the size of the libraries are limited and a deeper coverage of the proteome would increase the number of potential identifications in SWATH-MS analysis. In the present study, we produced spectral libraries for two well established models to study fruit ripening or animal embryogenesis, respectively Solanum lycopersicum L. and Drosophila melanogaster, for which no or low depth spectral libraries for SWATH-MS on TripleTOF instruments have been produced so far [17,18]. These libraries contain assays for more than 5,000 proteins for both species and are best suited...

The Generation of a Comprehensive Spectral Library for the Analysis of the Guinea Pig Proteome by SWATH‐MS

“…Interpretation of SWATH spectra, however, requires reference to a spectral library of peptide sequence matching (including established m / z and LC retention time co‐ordinates), itself oft‐obtained from the outcomes of multiple DDA runs. Spectral libraries of notable depth are available for only a few species (or specialized cells/tissues)—including human, mouse, a few microbiota, drosophila and tomato, zebrafish, and yeast—that, at present, limits the breadth of uptake of SWATH.…”

Generation of a murine SWATH-MS spectral library to quantify more than 11,000 proteins

“…Although a sample-specific spectral library can be generated, large previously established spectral libraries can offer more identifications and reduce the amount of samples and MS measurement time. The comprehensive spectral libraries for organisms such as human 13 , drosophila 14 , and zebrafish 15 have been published.…”

Large Scale Proteomic Data and Network-Based Systems Biology Approaches to Explore the Plant World

“…By means of MRMaid, the authors designed optimal transitions for 25 Arabidopsis thaliana proteins, and 23 of them were correctly quantified and validated. A spectral library of more than 5000 proteins was experimentally built for Solanum lycopersicum and optimized to be best suited in processing of DIA/SWATH data acquired on TripleTOF instruments [ 89 ]. A prior generation of a spectral library based on DDA data was also performed by Zhu et al to investigate inferior and superior rice spikelets during grain filling [ 90 ] and to understand the mechanisms underlying the molecular response of Arabidopsis thaliana to lead pollution [ 29 ].…”