This file has been created on 29-05-2024 by Christoph Bookmeyer. GENERAL INFORMATION ------------------ 1. Dataset title: Replication Data for: MASS2 - Modern Au-based Surfaces and Secondary ionisation for Mass Spectrometry Imaging of Small molecules 2. Authorship: Name: Christoph H.M. Bookmeyer Institution: Universitat Rovira i Virgili Email: christoph.bookmeyer@urv.cat ORCID: 0000-0002-3479-3841 DESCRIPTION ---------- 1. Dataset language: english 2. Abstract: Measurement raw data, experimental descriptions, and protocols created during the MSCA-PF-01 101067953 MASS2 - SALDI-SPICI-MSI. Measurements and optimization of Au-based surface-assisted laser desorption/ionization mass spectrometry imaging combined with single-photon induced chemical ionization. The project aimed to develop a novel means for extensive metabolome and lipidome analysis by SALDI-PI-MSI to overcome limitations of MALDI. For this,we combined of a new PI strategy coined Single-Photon Induced Chemical Ionisation (SPICI) with functionalised Au layers. With this, the chemical coverage of compounds in biomedical tissue sections could be extended, especially for an extended mass range below 500 Da, and with high mass and spatial resolution. The parameter were optimised and key settings for a comprehensive analysis identified. As a result, a large number of endogenous analytes were detected that could not be detected with conventional MALDI-MSI or SALDI-MSI systems before. Complex data outputs were analyzed with the versatile in-house developed software package rMSI that facilitated routine data mining. The new technical possibilities were demonstrated in the analysis and comprehensive spatial biochemical characterisation of zebra fish embryos. This can now serve as a fast and scalable template for, e.g., future toxicology/exposome studies. (2024-05-31) 3. Keywords: MSI - Mass spectrometry imaging MALDI - matrix-assisted laser desoprtion/ionization SALDI - surface-assisted laser desorption/ionization SPICI - single-photon induced chemical ionization 4. Date of data collection (single date or date range): 27-01-2023 - 26-04-2024 5. Publication Date: 29-07-2024 6. Grant information: Grant Agency: European Research Executive Agency (REA) Grant Number: HORIZON-MSCA-2021-PF-01 - 101067953 ACCESS INFORMATION ------------------------ 1. Creative Commons License of the dataset: CC-BY-NC 4.0 2. Dataset DOI: https://doi.org/10.34810/data1630 VERSIONING AND PROVENANCE --------------- 1. Last modification date: 16-08-2024 2. Were data derived from another source?: No. METHODOLOGICAL INFORMATION ----------------------- 1. Description of the methods used to collect and generate the data: Thin tissue sections were cryo-sectioned to a thickness of 10µm and thaw-mounted onto histological glass slides. The samples were covered with organic matrix using thermal evaporation and gas phase deposition, or covered with metal nanolayers. The samples were then measured with LDI-MSI (laser desorption/ionization mass spectrometry imaging). Technical parameters such as the in-source pressure, laser fluence, and laser repetition rate were varied on homogeneous tissue sections to determine the optimal conditions for target analytes. With the optimized protocol, MSI of model organisms were acquired. 2. Data processing methods: The raw data were converted to the open file format .imzml using the software ImageInsight (Spectroglyph, WA). The spectra acquired with different technical parameters were analyzed by statistical means, identifying classes of analytes that were detected with higher intensities at given parameter settings with our in-house data analysis software rMSI2. Furthermore, the spectra acquired with the same parameter settings at different time points were compared to assess the reproducibility of the measurement procedure. The data processing pipeline was exported as an .html file for the measured model organism. Furthermore, the data output was summarized in a pdf file. 3. Software or instruments needed to interpret the data: The raw data were converted to the open file format .imzml + .ibd, which can be read with several MSI data analysis softwares, (https://www.ms-imaging.org/imzml/), e.g., with the open source software rMSI2 (https://github.com/prafols/rMSI). 4. Information about instruments, calibration and standards: MS system: Dual-ion funnel/dual MALDI/ESI Injector (Spectroglyph, WA) coupled to an Exploris Orbitrap (Thermo Fisher Scientific, Germany) modified with a SPICI module (single-photon induced chemical ionization) for postionization. Metal nanolayers were deposited on microscopy glass slides with the sputtering system ATC Orion 8-HV (AJA International, N. Scituate, MA). The MS system was calibrated weekly as recommended by the vendor with FlexMix solution (Thermo Fisher Scientific, Germany) introduced via the ESI inlet in standard conditions. FILE OVERVIEW ---------------------- 1. Explain the file naming conversion, if applicable: the code of the data, e.g., 221021CB_Au_N_ZFE_unexp_S2_HPMC_x2_25um_60k first numbers are the acquisition date and the initials of the researcher CB the matrix: three figures positive or negative ion mode: P or N species: three figures conditions: e.g., unexp., cntr, or expo Slide-number S1, S2, .. (according to the numbering) (embedding media) position/section on the slide x1: up right, x10: bottom left pixel/step size in μm mass resolution (60k or 120k) abbreviations LMWC: optimized for low molecular weight compounds DDA: data-dependent acquisition parameter: the parameters were varied during the acquisition PI: Postionization matrix: DAN (Diaminonaphthalene), Au_ (Gold nanolayers), Ag_ (Silver nanolayers), DHB (2,5-dihydroxy benzoic acid) species: BLH: bovine liver homogenate; BBr: bovine brain; MBr: mural brain; RBr:rat brain; HBr: human brain; HLv: human liver; ZFE: zebrafish embryo; ZFH: zebrafish homogenate VxI: Extraction voltage of postionization ring, position 1 VxII: Extraction voltage of postionization ring, position 1 2. File list: File name: 240426CB_Au_P_PI_ZFE_unexp_HPMC_S4_x3_20um.imzml Description: raw data converted to the open source format File name: 240426CB_Au_P_PI_ZFE_exp_HPMC_S5_x8_20um_VxI.imzml Description: raw data converted to the open source format File name: 240426CB_Au_P_PI_ZFE_exp_HPMC_S5_x2_20um_VxI.imzml Description: raw data converted to the open source format File name: 240426CB_Au_P_PI_ZFE_exp_HPMC_S5_x1_20um_VxII.imzml Description: raw data converted to the open source format File name: 230322CB_Au_P_BBr_mid2_LMWC_60k_8t_800Hz_c.imzml Description: raw data converted to the open source format File name: 230322CB_Au_P_BBr_mid2_LMWC_60k_8t_800Hz_b.imzml Description: raw data converted to the open source format File name: 230322CB_Au_P_BBr_mid2_LMWC_60k_8t_800Hz_a.imzml Description: raw data converted to the open source format File name: 230322CB_Au_P_BBr_mid2_LMWC_60k_8t_600Hz_d.imzml Description: raw data converted to the open source format File name: 230322CB_Au_P_BBr_mid2_LMWC_60k_8t_600Hz_c.imzml Description: raw data converted to the open source format File name: 230322CB_Au_P_BBr_mid2_LMWC_60k_8t_600Hz_b.imzml Description: raw data converted to the open source format File name: 230322CB_Au_P_BBr_mid2_LMWC_60k_8t_600Hz_a.imzml Description: raw data converted to the open source format File name: 230322CB_Au_P_BBr_mid2_LMWC_60k_8t_500Hz_d.imzml Description: raw data converted to the open source format File name: 230322CB_Au_P_BBr_mid2_LMWC_60k_8t_500Hz_c.imzml Description: raw data converted to the open source format File name: 230322CB_Au_P_BBr_mid2_LMWC_60k_8t_500Hz_b.imzml Description: raw data converted to the open source format File name: 230322CB_Au_P_BBr_mid2_LMWC_60k_8t_500Hz_a.imzml Description: raw data converted to the open source format File name: 230322CB_Au_P_BBr_mid2_LMWC_60k_8t_400Hz_e.imzml Description: raw data converted to the open source format File name: 230322CB_Au_P_BBr_mid2_LMWC_60k_8t_400Hz_d.imzml Description: raw data converted to the open source format File name: 230322CB_Au_P_BBr_mid2_LMWC_60k_8t_400Hz_c.imzml Description: raw data converted to the open source format File name: 230322CB_Au_P_BBr_mid2_LMWC_60k_8t_400Hz_b.imzml Description: raw data converted to the open source format File name: 230322CB_Au_P_BBr_mid2_LMWC_60k_8t_400Hz_a.imzml Description: raw data converted to the open source format File name: 230322CB_Au_P_BBr_mid2_LMWC_60k_8t_200Hz_c.imzml Description: raw data converted to the open source format File name: 230322CB_Au_P_BBr_mid2_LMWC_60k_8t_200Hz_b.imzml Description: raw data converted to the open source format File name: 230322CB_Au_P_BBr_mid2_LMWC_60k_8t_200Hz_a.imzml Description: raw data converted to the open source format File name: 230127CB_Au_P_BBr_mid3_x6_30um_60k_LMWC.imzml Description: raw data converted to the open source format File name: 230127CB_Au_P_BBr_mid3_x5_30um_60k_LMWC.imzml Description: raw data converted to the open source format File name: 230127CB_Au_P_BBr_mid3_x4_30um_60k_LMWC.imzml Description: raw data converted to the open source format File name: 230127CB_Au_P_BBr_mid3_x2_30um_60k_LMWC.imzml Description: raw data converted to the open source format File name: 230127CB_Au_P_BBr_mid3_x1_30um_60k_LMWC.imzml Description: raw data converted to the open source format File name: 230127CB_Au_P_BBr_mid2_x7_30um_60k_LMWC.imzml Description: raw data converted to the open source format File name: 230127CB_Au_P_BBr_mid2_x6_30um_60k_LMWC.imzml Description: raw data converted to the open source format File name: 230127CB_Au_P_BBr_mid2_x5_30um_60k_LMWC.imzml Description: raw data converted to the open source format File name: 230127CB_Au_P_BBr_mid2_x4_30um_60k_LMWC.imzml Description: raw data converted to the open source format File name: 230127CB_Au_P_BBr_mid2_x3_30um_60k_LMWC.imzml Description: raw data converted to the open source format File name: 230127CB_Au_P_BBr_mid2_x1_30um_60k_LMWC.imzml Description: raw data converted to the open source format File name: 240426CB_Au_P_PI_ZFE_unexp_HPMC_S4_x3_20um.ibd Description: raw data converted to the open source format File name: 240426CB_Au_P_PI_ZFE_exp_HPMC_S5_x8_20um_VxI.ibd Description: raw data converted to the open source format File name: 240426CB_Au_P_PI_ZFE_exp_HPMC_S5_x2_20um_VxI.ibd Description: raw data converted to the open source format File name: 240426CB_Au_P_PI_ZFE_exp_HPMC_S5_x1_20um_VxII.ibd Description: raw data converted to the open source format File name: 230322CB_Au_P_BBr_mid2_LMWC_60k_8t_800Hz_c.ibd Description: raw data converted to the open source format File name: 230322CB_Au_P_BBr_mid2_LMWC_60k_8t_800Hz_b.ibd Description: raw data converted to the open source format File name: 230322CB_Au_P_BBr_mid2_LMWC_60k_8t_800Hz_a.ibd Description: raw data converted to the open source format File name: 230322CB_Au_P_BBr_mid2_LMWC_60k_8t_600Hz_d.ibd Description: raw data converted to the open source format File name: 230322CB_Au_P_BBr_mid2_LMWC_60k_8t_600Hz_c.ibd Description: raw data converted to the open source format File name: 230322CB_Au_P_BBr_mid2_LMWC_60k_8t_600Hz_b.ibd Description: raw data converted to the open source format File name: 230322CB_Au_P_BBr_mid2_LMWC_60k_8t_600Hz_a.ibd Description: raw data converted to the open source format File name: 230322CB_Au_P_BBr_mid2_LMWC_60k_8t_500Hz_d.ibd Description: raw data converted to the open source format File name: 230322CB_Au_P_BBr_mid2_LMWC_60k_8t_500Hz_c.ibd Description: raw data converted to the open source format File name: 230322CB_Au_P_BBr_mid2_LMWC_60k_8t_500Hz_b.ibd Description: raw data converted to the open source format File name: 230322CB_Au_P_BBr_mid2_LMWC_60k_8t_500Hz_a.ibd Description: raw data converted to the open source format File name: 230322CB_Au_P_BBr_mid2_LMWC_60k_8t_400Hz_e.ibd Description: raw data converted to the open source format File name: 230322CB_Au_P_BBr_mid2_LMWC_60k_8t_400Hz_d.ibd Description: raw data converted to the open source format File name: 230322CB_Au_P_BBr_mid2_LMWC_60k_8t_400Hz_c.ibd Description: raw data converted to the open source format File name: 230322CB_Au_P_BBr_mid2_LMWC_60k_8t_400Hz_b.ibd Description: raw data converted to the open source format File name: 230322CB_Au_P_BBr_mid2_LMWC_60k_8t_400Hz_a.ibd Description: raw data converted to the open source format File name: 230322CB_Au_P_BBr_mid2_LMWC_60k_8t_200Hz_c.ibd Description: raw data converted to the open source format File name: 230322CB_Au_P_BBr_mid2_LMWC_60k_8t_200Hz_b.ibd Description: raw data converted to the open source format File name: 230322CB_Au_P_BBr_mid2_LMWC_60k_8t_200Hz_a.ibd Description: raw data converted to the open source format File name: 230127CB_Au_P_BBr_mid3_x6_30um_60k_LMWC.ibd Description: raw data converted to the open source format File name: 230127CB_Au_P_BBr_mid3_x5_30um_60k_LMWC.ibd Description: raw data converted to the open source format File name: 230127CB_Au_P_BBr_mid3_x4_30um_60k_LMWC.ibd Description: raw data converted to the open source format File name: 230127CB_Au_P_BBr_mid3_x2_30um_60k_LMWC.ibd Description: raw data converted to the open source format File name: 230127CB_Au_P_BBr_mid3_x1_30um_60k_LMWC.ibd Description: raw data converted to the open source format File name: 230127CB_Au_P_BBr_mid2_x7_30um_60k_LMWC.ibd Description: raw data converted to the open source format File name: 230127CB_Au_P_BBr_mid2_x6_30um_60k_LMWC.ibd Description: raw data converted to the open source format File name: 230127CB_Au_P_BBr_mid2_x5_30um_60k_LMWC.ibd Description: raw data converted to the open source format File name: 230127CB_Au_P_BBr_mid2_x4_30um_60k_LMWC.ibd Description: raw data converted to the open source format File name: 230127CB_Au_P_BBr_mid2_x3_30um_60k_LMWC.ibd Description: raw data converted to the open source format File name: 230127CB_Au_P_BBr_mid2_x1_30um_60k_LMWC.ibd Description: raw data converted to the open source format File name: 231018_Au_P_MBr_ITO_Alu_cblm.html Description: The data processing pipeline for Au-sputtered sections of a mouse brain on an ITO slide was exported as an .html file File name: 231018_Au_P_MBr_ITO_Alu_LMWC_MSI_o_Ac.html Description: The data processing pipeline for Au-sputtered sections of a mouse brain on an ITO slide without acetone was exported as an .html file File name: Zebrafish_analysis_Au_lipids.html Description: The data processing pipeline for Au-sputtered sections of zebra fish embryos was exported as an .html file File name: Code for measurements Description: The code used for the naming of the files of measurements File name: record of measurement results and validation of stability.pdf Description: record of measurement results and validation of stability for all measured model organism within the project, summarized in a pdf file. File name: 2024_CB_Milab_sample preparation MSI guide.pdf Description: A guide for the sample preparation developed in the project and used for all the measured samples in a pdf file 3. Relationship between files: imzml. files are to be combined with the corresponding .ibd file html and pdf show summaries of the analyzed data (records of measurements) as well as the sample preparation guide and the code for the measurements (protocols) 4. File formats: imzml, ibd html; pfd 5. If the dataset includes multiple files, specify the directory structure and relationships between the files: The data set includes raw measurement data converted to the open format .imzml+.ibd, records of measurements, and measurements protocols.