Proteome data of serum samples from patients with schizophrenia

Schizophrenia is a complex chronic disease. The molecular determinants and neuropathology of schizophrenia are multifaceted; an important role in the pathogenesis is played by the dysregulation of molecular and epigenetic mechanisms. However, the molecular mechanisms of the development of the disease have not yet been studied. An important task is the accumulation and systematization of “OMICS”-knowledge of the molecular profiles (transcriptome, proteome, metabolome) of blood specific to pathology. Thereby the development and improvement of mass spectrometric methods for the detection of biological molecules has become increasingly important in biomedical research. In the field of applied problems in biomedical research, the most prevalent issue involves the identification of serological protein markers associated with the development of schizophrenia, which account for the diseases that cause the a life-shortening illness, disability, decreased of functioning and quality of life and wellbeing or health status. OMICS approaches are designed to detect genes (genomics), mRNA (transcriptomics), proteins (proteomics) and metabolites (metabolomics) in a specific biological sample. We report the proteomic datasets on the serum samples from patients with schizophrenia (series “SCZ”) and healthy volunteers (series “CNT”). Data were acquired using shotgun ultra-high resolution mass spectrometry.


a b s t r a c t
Schizophrenia is a complex chronic disease. The molecular determinants and neuropathology of schizophrenia are multifaceted; an important role in the pathogenesis is played by the dysregulation of molecular and epigenetic mechanisms. However, the molecular mechanisms of the development of the disease have not yet been studied. An important task is the accumulation and systematization of "OMICS"-knowledge of the molecular profiles (transcriptome, proteome, metabolome) of blood specific to pathology. Thereby the development and improvement of mass spectrometric methods for the detection of biological molecules has become increasingly important in biomedical research. In the field of applied problems in biomedical research, the most prevalent issue involves the identification of serological protein markers associated with the development of schizophrenia, which account for the diseases that cause the a life-shortening illness, disability, decreased of functioning and quality of life and wellbeing or health status. OMICS approaches are designed to detect genes (genomics), mRNA (transcriptomics), proteins (proteomics) and metabolites (metabolomics) in a specific biological sample. We report the proteomic datasets on the serum samples from patients with schizophrenia (series "SCZ") and healthy volunteers (series "CNT"). Data were acquired using shotgun ultra-high resolution mass spectrometry.
© 2020 The Authors. Published by Elsevier Inc. This is an open access article under the CC BY license (http://creativecommons. org/licenses/by/4.0/).

Data description
The dataset contains "*.raw " and "*.mgf " data obtained through the shotgun HPLC-MS/MS analysis of serum samples from 49 patients with schizophrenia and 50 healthy volunteers. Data are available via ProteomeXchange with identifier PXD016297 [1]. Information about blood samples collected from patients with schizophrenia and control samples from healthy donors is presented in Table 1. Dataset covers 99 biological samples (see Table 2).

Reagents
Acetonitrile and TCA were from Merck (Germany). Formic acid was from ACROS Organics (USA). Ethylenediaminetetraacetic acid (EDTA) was from Sigma-Aldrich (USA). Modified trypsin was from Specifications Table   Subject Biology Specific subject area Biochemistry, omics analysis, protein detection Type of data Value of the Data Dataset represents proteomes of serum samples from patients with schizophrenia as well as from control healthy volunteers, which can be compared to reveal molecular pathways of pathology. Blood plasma serves as an attractive source of candidate protein markers and specific pathologies for molecular profiling, as it contains molecular components secreted by cells in diseased tissues, as well as factors involved in the development of pathophysiological processes. Protein profiling are perspective to reveal for clinical monitoring of drug therapy, for identification of affected signalling pathways may indicate the direction of research for the development of a systematic approach to the diagnosis and classification of schizophrenia disease. Protein profiles are available in the form of "*.raw" and "*.mgf" data that can be further processed by researchers using their own bioinformatics algorithms and analysed together with their own data.

BioSamples
These data include patients with a diagnosis of schizophrenia and healthy controls, all participants signed the informed consent form.
The group of patients: 49 patients (26 men, 23 women, average age 26.9 ± 5.2 years) who were hospitalized in State Healthcare Institution «Psychiatric Clinical Hospital 1 n. a. N.A. Alekseev of Healthcare Department of Moscow» from February to April 2019 with a diagnosis of schizophrenia.
The control group consisted of 50 volunteers from among employees, students and residents who have never sought psychiatric help and who are not related to patients.

Age 18 or older 2. Male or female 3. Diagnosis of schizophrenia
The diagnosis of schizophrenia was established on the basis of the criteria of the International Classification of Diseases of the 10th revision (ICD-10) (see Table 3).

Non-inclusion criteria
1. Organic disease of the central nervous system; 2. Decompensation of somatic disease;  The clinical and psychometric methods used in the practice of research on mental pathology were used. A single examination of patients involves: -psychopathological and somatic examination; -psychometric examination using standardized international scales (PANSS, FAB, NSA-4, BFCRS)  Blood sampling (8e12 ml) was carried out in vacuum tubes with heparin in a treatment room in compliance with aseptic and antiseptic rules. Transportation to the laboratory was carried out within 2 hours from the moment of collection. Blood sampling was carried out once between 8 and 9 a.m. in the clinic's treatment rooms from a cubital vein into tubes with EDTA and a gel separator, followed by centrifugation of 2000 rpm for 20 minutes. The isolated serum was stored in eppendorf type microtubes at À80, whole blood was stored at À20 until transported to the laboratory. Transportation was carried out in compliance with material safety requirements.

Sample preparation for MS analysis
The blood plasma in the volume of 40 ml was then brought to the final volume of 160 ml by adding the solution 15 mM MOPS (4-morpholinepropanesulfonic acid sodium salt), рН 7.4.
The dry residue was restored in 500 ml of 0.1% deoxycholic acid sodium salt, 6% acetonitrile, 75 mM triethylammonium bicarbonate, рН 8.5. The protein solution was heated up at 90 C for 10 minutes at intensive shaking (1100 rpm). After equilibration to ambient temperature, 3 mM ТСЕР (Tris (2carboxyethyl)phosphine) was added to the denatured protein solution to restore the sulfhydryl groups of amino-acid residues of cysteine. The reaction was incubated at 45 C for 20 minutes. For alkylation, the denatured protein solution was added with a solution of 0.2% 4-vinylpyridine in 30% propan-2-ol up to a final concentration of 0.02% (V/V). The alkylation reaction was carried out for 30 minutes at normal temperature in the lightproof place.
Enzymatic cleavage of proteins was performed using a specific trypsin protease. The protein solution was added with modified (acetylated at primary amino groups of lysine) trypsin at enzyme-tosubstrate ratio as 1:50. The reaction was incubated at 42 C for 4 hours with intermittent mixing for 3 minutes every 15 minutes. After that, the second aliquot of trypsin was added at ration 1:100 and incubated at 37 C continued for additional 12 hours.
Upon the time expiry the enzyme reaction was inhibited by adding the formic acid up to the final concentration of 0.5%, which also caused precipitation of insoluble deoxycholic acid. The obtained suspended solids were centrifuged at 12,000 rpm at 15 C for 10 minutes. The supernatant (approximately 550 ml) was collected and applied to Discovery DSC solid-phase columns, which were preliminary equilibrated with the solution of 2% methanol with 0.1% formic acid. After sample application the columns were washed twice with 1 ml of 0.1% formic acid solution, and then peptides were eluted from the carrier using the solution of 70% methanol with 5% formic acid in the volume of 1 ml. The collected Eliot was dried at 30 C for 45 minutes in a vacuum. The dry residue was restored in 40 ml of 0.5% formic acid solution and transferred into vials of deactivated glass for mass spectrometry analysis [2,3].

Mass spectrometry protein registration
The mass spectrometric analysis of the peptide composition of plasma samples was conducted for depleted plasma samples. HPLC-MS/MS registration of peptides was carried out using high resolution mass spectrometer Q Exactive (Thermo Scientific, USA, Catalog # IQLAAEGAAPFALGDK) by chromatographic separation using Ultimate 3000 Nano-flow HPLC system (Thermo Scientific, USA, Catalog # ULTIM3000RSLCNANO). Peptides in the volume of 5 ml were applied on enrichment column PepMap C18 for 4 minutes in the isocratic flow of the mobile phase C (2% acetonitrile, 0.08% formic acid, 0.015% trifluoroacetic acid) at a flow rate of 20 ml/min. Peptides were separated using Acclaim PepMap C18 analytical column (75 mm Â 150 mm, particle size 2 mm, pore size 100 A) in the nano-flow mode in the linear gradient of the mobile phase A (0.08% formic acid, 0.015% trifluoroacetic acid) and the mobile phase B (0.08% formic acid, 0.015% trifluoroacetic acid in acetonitrile) at a flow rate of s400 nl/min at initial ratio А: В as 98:2. Separation was performed in the elution gradient from 2% to 35% of mobile phase B content for 80 minutes, followed by column washing at 90% of phase B for 10 minutes with subsequent system equilibration at initial gradient conditions for 20 minutes.
Registration of peptide signal was carried out in the dependent tandem scan mode with ionization source NSI (Thermo Scientific, USA). After rescanning of precursor ions with maximum accumulation time not more than 80 ms (or maximum accumulation value 3е6) with resolution R ¼ 70 K in the range of 420e1250 m/z, 20 sequential tandem scans were made with maximum accumulation time not more than 120 ms (or maximum accumulation value 1е5) with resolution R ¼ 17.5 K a with fixed minimum range value (from 220 m/z) and varying maximum range value depending on the resolved charge state. Ions with charge state z ¼ 2þ … 5þ were selected for tandem scanning using the dynamic exclusion for the duration of one half-width of the chromatographic peak. Isolation of precursor ions was performed with the width of w ¼ ±1 Th within the range from 9 to 17 s from the peak apex for the tandem scanning. Fragmentation was performed in the high-energy activation mode (HCD e Higher-energy collisional dissociation) with rating 27% (per weight of 400 m/z and charge z ¼ 2þ) and variation per each scanning within ±15%. HPLC-MS/MS spectra in RAW format were processed in Mass Hunter version В 2.0 [2,3].