Citation: Novikova, S.; Soloveva, N.; Farafonova, T.; Tikhonova, O.; Shimansky, V.; Kugushev, I.; Zgoda, V. Proteomic Shotgun and Targeted Mass Spectrometric Datasets of Cerebrospinal Fluid (Liquor) Derived from Patients with Vestibular Schwannoma. Data 2023, 8, 71. https://doi.org/10.3390/ data8040071 Academic Editor: Pufeng Du Received: 3 March 2023 Revised: 31 March 2023 Accepted: 4 April 2023 Published: 6 April 2023 Copyright: © 2023 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https:// creativecommons.org/licenses/by/ 4.0/). data Data Descriptor Proteomic Shotgun and Targeted Mass Spectrometric Datasets of Cerebrospinal Fluid (Liquor) Derived from Patients with Vestibular Schwannoma Svetlana Novikova 1, *, Natalia Soloveva 1 , Tatiana Farafonova 1 , Olga Tikhonova 1 , Vadim Shimansky 2, *, Ivan Kugushev 2 and Victor Zgoda 1, * 1 Institute of Biomedical Chemistry, 119121 Moscow, Russia 2 N.N. Burdenko National Scientific and Practical Center for Neurosurgery, 125047 Moscow, Russia * Correspondence: novikova@ibmc.msk.ru (S.N.); shimava@nsi.ru (V.S.); vic@ibmc.msk.ru (V.Z.); Tel.: +7-499-246-69-80 (V.Z.) Abstract: Vestibular schwannomas are relatively rare intracranial tumors compared to other brain tumors. Data on the molecular features, especially on schwannoma proteome, are scarce. The 41 cerebrospinal fluid (liquor) samples were obtained during the surgical removal of vestibular schwannoma. Obtained peptide samples were analyzed by shotgun LC-MS/MS high-resolution mass spectrometry. The same peptide samples were spiked with 148 stable isotopically labeled peptide standards (SIS) followed by alkaline fractionation and scheduled multiple reaction monitoring (MRM) for quantitative analysis. The natural counterparts of SIS peptides were mapped onto 111 proteins that were Food and Drug Administration (FDA)-approved for diagnostic use. As a result, 525 proteins were identified by shotgun LC-MS/MS with high confidence (at least two peptides per protein, FDR < 1%) in liquor samples. Absolute quantitative concentrations were obtained for 54 FDA- approved proteins detected in at least five experimental samples. Since there is lack of data on the molecular landscape of vestibular schwannoma, the obtained datasets are unique and one of the first in its field. Dataset: http://www.peptideatlas.org/PASS/PASS04821, http://www.proteomexchange.org/ (Project identifier: PXD037746). Dataset License: CC-BY Keywords: mass spectrometry; proteomics; shotgun; targeted mass spectrometry; MRM/SIS; vestibular schwannoma 1. Summary Vestibular schwannomas are neurological tumors that account for about 5–8% of all intracranial tumors [1]. The disease is usually diagnosed at the relatively young age of 50–60 years and the surgical removal of tumors can be complicated by meningitis, cerebellar injury, epilepsy, and persistent headaches [2]. Due to the rarity and heterogeneity of this tumor, there is lack of data on the special molecular feature of vestibular schwannoma [2], including data on vestibular schwannoma proteome. The cerebrospinal fluid (CSF) contains various biomolecules, e.g., ctDNA, micro RNA, and proteins, which reflect the molecular landscape of the liquor [3]. Of the variety of biological molecules, proteins represent the physical basis of the phenotype. CFS samples can be obtained via lumbar puncture or brain surgery. Thus, CSF represents an appealing source of potential protein biomarkers. High throughput shotgun mass spectrometry, which has been rapidly developing in recent years, allows the identification of hundreds of proteins in one experiment [4]. The Data 2023, 8, 71. https://doi.org/10.3390/data8040071 https://www.mdpi.com/journal/data