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Abstract Data-Independent Acquisition (DIA) is a mass spectrometry-based method to reliably identify and reproducibly quantify large fractions of a target proteome. The peptide-centric data analysis strategy employed in DIA requiresa priorigenerated spectral assay libraries. Such assay libraries allow to extract quantitative data in a targeted approach and have been generated for human, mouse, zebrafish,E. coliand few other organisms. However, a spectral assay library for the extreme halophilic archaeonHalobacterium salinarumNRC-1, a model organism that contributed to several notable discoveries, is not publicly available yet. Here, we report a comprehensive spectral assay library to measure 2,563 of 2,646 annotatedH. salinarumNRC-1 proteins. We demonstrate the utility of this library by measuring global protein abundances over time under standard growth conditions. TheH. salinarumNRC-1 library includes 21,074 distinct peptides representing 97% of the predicted proteome and provides a new, valuable resource to confidently measure and quantify any protein of this archaeon. Data and spectral assay libraries are available via ProteomeXchange (PXD042770, PXD042774) and SWATHAtlas (SAL00312-SAL00319).
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Comprehensive spectral libraries for various rabbit eye tissue proteomes
Abstract Rabbits have been widely used for studying ocular physiology and pathology due to their relatively large eye size and similar structures with human eyes. Various rabbit ocular disease models, such as dry eye, age-related macular degeneration, and glaucoma, have been established. Despite the growing application of proteomics in vision research using rabbit ocular models, there is no spectral assay library for rabbit eye proteome publicly available. Here, we generated spectral assay libraries for rabbit eye compartments, including conjunctiva, cornea, iris, retina, sclera, vitreous humor, and tears using fractionated samples and ion mobility separation enabling deep proteome coverage. The rabbit eye spectral assay library includes 9,830 protein groups and 113,593 peptides. We present the data as a freely available community resource for proteomic studies in the vision field. Instrument data and spectral libraries are available via ProteomeXchange with identifier PXD031194.
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- Award ID(s):
- 2005199
- PAR ID:
- 10364611
- Publisher / Repository:
- Nature Publishing Group
- Date Published:
- Journal Name:
- Scientific Data
- Volume:
- 9
- Issue:
- 1
- ISSN:
- 2052-4463
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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