BafPipe

Automated deconvolution of mass spectra datasets using UniDec.

Cite Marty et al. Anal. Chem. 2015. DOI: 10.1021/acs.analchem.5b00140

Automates the UniDec deconvolution algorithms for large Bruker mass spectra datasets and quantifies relative peak intensity. Converts Bruker .baf to numpy arrays using baf2sql and then automates unidec to deconvolute protein mass spectra and quantify species.

pip install BafPipe

The software uses an input excel file containing deconvolution parameters, species identities/masses and data plotting parameters.

Setting up the input file

Sheet 1 of input file contains the directory folder of your mass spectra and the unidec configuration parameters.

You can also add masses to detect and a corresponding colour. These are done by stipulating Species + name and Color + name in the Parameter column, followed by the desired mass or colour in the Input column.

Example input directory

Each file within the directory can be linked to custom variables defined in a second sheet of the input directory. This comes in handy if wanting to filter data or perform analyses/comparison on subsets of your experiment.

Any column names can be defined aside from 'Name' in column 0. Name corresponds to your filename (can be partial match).

Make sure var_ids=True load_input_file(var_ids = True)

Example variables table

Running the code

from bafpipe.pipe import *

path = r"C:\users\input_file.xlsx

bafpipe = on_bafpipe(path)

Quantified results will be exported to Excel results table containing MS metadata from .xml (including aquisition time, e.g. for kinetics/real time MS)

Other functions:

loading input file with var IDs:

from bafpipe.ms_processing import * eng = BafPipe() eng.load_input_file(path, unzip=False, clearhdf5=True, var_ids=True) eng.on_unidec()

This will export quantified results to the Excel results table with additional sample metadata.