msac 0.1.0

Molecular Spectrometry Adduct Calculator: Calculates m/z of potential adducts given compound m/z

Molecular Spectrometry Adduct Calculator (MSAC)

The Molecular Spectrometry Adduct Calculator (MSAC) calculates the m/z of potential adducts from given compound m/z. This can help in reading a mass spectrometry spectra. The user provides a .csv with one column containing monoisotopic masses titled 'mass'; other columns will be preserved. Optionally, the user can also supply a more targeted list of adducts to calculate: a .csv with columns 'adduct' and 'charge', where adducts are written without brackets such as M+Na or M-H.

Getting Started

These instructions will get you to run the calculator as a python package.

Prerequisites

Recommended installation is through anaconda, so dependencies are compatible with each other.

Dependencies are pandas, numpy, and molmass.

Using conda:

conda env create -f msac-env.yml
conda activate msac-env

A requirements.txt file is also available.

Installing

In your activated conda environment, install the calculator.

# clone/install
git clone https://github.com/pnnl/msac.git
pip install msac/

# direct
pip install git+https://github.com/pnnl/msac

Running the calculator

MSAC is provided with two adduct lists: a default list of 13 common adducts and an extensive list of adducts found in NIST17. To calculate the m/z for these adducts based on your input masses, pass MSAC a .csv with the compound masses in a column titled 'mass'. Other columns present in the file will be preserved.

msac input.csv

If your input file's monoisotopic mass column is not called 'mass', you can pass in the title as a string.

msac input.csv -m "Monoisotopic Mass"

You can also specify an output file name; default is {input_name}_adducts.csv.

msac input.csv -o my_output_name.csv

If you want to use your own list of adducts, create a csv with a column called 'adduct' and an column of 'charge'. Check example_data/adduct_list_full.csv for an example. The default adduct list included in the distribution is used here.

msac input.csv -f adduct_only_list.csv

If you want to include potential neutral losses, add the -n flag.

msac input.csv -n

If you're using the default adduct list or the neutral loss list with -n, you can limit the number of adducts used based on its prevalence in NIST/GNPS/MassBank. Using a value 1.0 or less will give you all adducts that cover more than the specified percent of NIST/GNPS/MassBank. Using an integer value 2+ gives that number of adducts.

msac input.csv -c 0.75 -o "75th_percentile_adducts.csv"
msac input.csv -c 5 -o "top_5_most_common_adducts.csv"

If you have a column of formulas in your input file, you can have MSAC calculate the input masses for you and/or have it output 'NaN' values when a neutral loss cannot be done due to the number of atoms in the molecule.

# have MSAC calculate the mass using --formula_col
msac input.csv -f "Formula"
# have MSAC restrict losses to those numerically possible using --restrict
msac input.csv -r "Formula"

Authors

• Madison Blumer

License

This project is licensed under the BSD License - see the LICENSE.md file for details

Acknowledgments

• Thank you to PurpleBooth for a great README template.