Software and code for the MS Data analysis as described in the article "Amino acids catalyse RNA formation under ambient alkaline conditions" by Dr. Saroj K. Rout, Mr. Sreekar Wunnava, Dr. Miroslav Krepl, Dr. Giuseppe Cassone, Dr. Judit E. Šponer, Dr. Christof B. Mast, Prof. Matthew W. Powner and Prof. Dieter Braun. The preprint is available on Research Square at https://doi.org/10.21203/rs.3.rs-4343389/v1. The manuscript is in revision at Nature Communications.

This work was supported by the European Research Council (ERC) Evotrap, grant no. 787356 (D.B., S.W.); the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation)—Project-ID 364653263—TRR 235 (CRC 235) (D.B., S.W., C.B.M.) and Project-ID 521256690 —TRR 392 (CRC 392) (D.B., S.W., C.B.M., S.K.R.), the Simons Foundation (grant no. 327125) (D.B.), the Excellence Cluster ORIGINS funded by Germany’s Excellence Strategy EXC-2094-390783311 (D.B., C.B.M., S.K.R.), support from the Volkswagen Foundation (D.B., C.B.M. and M.W.P.), the Czech Science Foundation (GAČR grant. no. 22-25057S) (J.E.S.) and the Swiss National Science Foundation (grant no. 206871) (S.K.R.).

Contact person for the project:

Prof. Dieter Braun,
Fakultät für Physik,
Ludwig-Maximilians-Universität München
Geschwister-Scholl-Platz 1
80539 München

The data stored in the research data repository of the University Library of Munich (Open Data LMU) as a 7z file is composed as follows:

1. Readme-Spectral Browser_3.58b.txt: Contains the installation and usage guide for the Spectral_Browser_3.58b

2. Spectral_browser_3.58b.zip: Zip file containing the main LabView code VI "Spectral_browser_3.58.vi" and a folder "TOF_sibVIs" containing the subVIs and dependencies. Note: Requires LabView 2014 64bit (Not provided).

3. pwiz-setup-3.0.21188.d133fbefc-x86_64.msi: Setup file for the ProteoWizard version used in the analysis.

4. Anaconda3-2021.05-Windows-x86_64.exe: Setup file for Anaconda3 to streamline the Python installation. Other installation of Python also work.

5. labview-zmq-3.3.1.102.vip: LabView package for installing LabVIEW bindings for zeromq.

6. Labview-Python-Server-2.4.exe: Self-made executable file that runs the zeromq communication link between LabView and Python running IsoSpecPy.

7. isotope_definitions.json: Definition file for the labelled isotopes C13, N15 etc. used by the LabView-Python-Server-2.4.exe when defining molecules with isotope labels in the Spectral_browser_3.58 for MS analysis. 

8: Example folder: This folder contains LC-MS data corresponding to one of the replicates used in the Figure 4b-e. The raw data acquired by the Agilent MassHunter acquisition software is saved in ".d" format ("GCAU-Val-p10t25-dry20h-2.d)". Using MSConvertGUI (Part of the ProteoWizard), ".d" format is converted to ".mz5" format. The "Config.all" file is loaded in the Spectral_browser_3.58.vi along with the mz5 format. Config file saves the different analysis parameters for the dataset including the retention time cursors. Upon analysis of the ".mz5" file in the Spectral browser, a ".bis" file is generated which saves the analyzed data in a binary format for faster retrieval.