This program is designed to create an in silico MS2 library for lipidomic analysis.

You can find our ArchLips MS2 library (.msp format) in: https://doi.org/10.5281/zenodo.16040382

To use this library, you can cite:

A comprehensive database for high-throughput identification of archaeal lipids using high-resolution mass spectrometry

https://doi.org/10.1038/s41467-025-67286-3

• Statistic Sheet: Save the additional information of the molecules: eg., Formula, inchi, Smile, references. This information will not affect the exportation result.

• Export Controller Sheet: This sheet decides which sheets will be exported. The sheet number of the MS2 sheet is recorded in column A (the sheet name can be recorded in column B for clarity). The exportation program reads the maximum and minimum values in column A, and the data sheets in between will be exported.

• Data Sheets:

• The first 5 rows record the general information of this molecule and the sheet. and the 6th row records the title of the column
• Start from the 7th row, each row records an individual molecule to be exported.
• The first 28 columns (A to AB) represent the general information of the molecules and the structural information to be exported.
• The peak information (X peaks) of the molecules’ MS2 is saved in the following peak columns. Columns from 29 to 28+X record the m/z value of the peak, and columns from 29+X to 28+2*X record the peak height. In one datasheet, all molecules should have the same peak columns. A 0 value can be used and will be ignored during the exportation.

• This program is up-to-date to work with Python 3.12
• tqdm (https://github.com/tqdm/tqdm）
• openpyxl (https://openpyxl.readthedocs.io/)

pip install tqdm
pip install openpyxl

Save your data file in the folder: Files_for_construction. Then you can export the library by running the PoolExport.py script with the default setting. The exported .msp library files can be found in Exported_msp folder.

python PoolExport.py

• --folder_path: Specify the directory of the .xlsm data files.
• --include_path: "1" only read the datafile in folder_path. "2" also read the datafile in the subfolders of the folder_path (default: 2).
• --export_path: Specify the directory of the exportated files.
• --standardization: "True": Standardize the MS2 in the MSP library, unify the maximum peak, remove replicate peaks, and remove low peaks. "False": Do not standardize the MS2.
• --max_peak: Maximum peak height after standardization (default: 1000).
• --min_peak: Peak height below will be filtered (default: 0.1).
• --merge_at_end: "True": Combine all exported .msp files into one .msp file. "False": Do not combine files (default: False).
• --merge_while_processing (More efficient than merge_at_end method, but the result file will not in the original order): True: Combine files while exporting files (default: True).
• --delete_intermediate: "True": Delete intermediate files (default: False).
• --threads: Threads number used in this exportation. Use "0" for the maximum threads (default: 0).

• import_adduct(): Specify the adduct ion of the library to be exported.

• single_msp_export(): Lines 49-62 specify the structural information in the data file to be exported.

This program is inspired and modified from Lipidblast. https://fiehnlab.ucdavis.edu/projects/LipidBlast