MassIVE MSV000101199

Partial Public PXD076015

DIA-PASEF proteomics of atlantic herring somatic tissues with focus on LRRC8C ion channel proteoforms

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Description

This is part of a project on the evolution of the Atlantic herring, focusing on the adaptation of its reproductive system to the lower salinity of the Baltic Sea. The LRRC8C ion channel is believed to produce genetic variants that confer reproductive advantages to local herring populations. In this study, we present DIA-PASEF proteomics data for Atlantic herring tissues, including the brain, heart, spleen, liver, and somatic muscle. These data were searched directly against the corresponding genomic database, which was supplemented with LRRC8C ion channel proteoforms. Samples were lysed in 2% SDS, 100 mM HEPES in Barocycler 2320XT and then tryptically digested by SP3 on Resyn Amine Beads in Kingfisher Duo Prime with spiking with Biognosys iRT peptide standard. Mass spectrometric analysis was done by data-independent acquisition (DIA) on Bruker timsTOF Pro (400 ng equivalent loaded, 100 min gradient, 20x2 variable window diaPASEF method, 2 technical replicates per sample). Data processing was done by Biognosys Spectronaut v20.2. Protein identification and spectral library generation from DIA experiments was implemented using Pulsar search engine against UniProtKB Clupea harengus reference proteome v8.2023 with default parameters with 8 additional entries for LRRC8C proteoforms plus 54 protein in-house contaminant database, all 1% FDR. DIA quantification was done using up to 6 fragments per peptide, up to 10 peptides per proteins, dynamic retention time alignment, dynamic mass recalibration and quartile normalization, 1% FDR and global data imputation for final results table. [doi:10.25345/C5QZ22X2B] [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: atlantic herring, proteomics, DIA-PASEF, brain, heart, spleen, liver, muscle, LRRC8C ; DatasetType:Proteomics

Contact

Principal Investigators:
(in alphabetical order) 		Prof. Henning Urlaub, Max Planck Institute for Multidisciplinary Sciences, Germany
Submitting User: sergey_moshkovskiy

Publications

Ma C, Sangdehi FM, Kawaguchi M, Sano K, Dannenberg SV, Pettersson ME, Wallberg A, Wort JL, Yan Y, Moshkovskii S, Berg F, Folkvord A, Lenz C, Urlaub H, Kaupp UB, Yasumasu S, Andersson L.
Sperm, egg, and embryo proteins critical for genetic adaptation of herring to low salinity in the Baltic Sea.
Proc Natl Acad Sci U S A. 2026 May 19;123(20):e2601861123. Epub 2026 May 11.

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