mzMLb things

[wkumler]

mzMLb tasks:

• [x] Conversion code (implemented in msconvert already)
• [x] Single spectrum
• [x] Chromatogram (given m/z range)
• [x] Multi-spectrum RT range

Exactly the same as mzML except for the filename and the parser

[wkumler]

Chromatogram extraction function below:

import matplotlib.pyplot as plt
from pyteomics import mzml, mzmlb
import numpy as np
import pandas as pd

def get_chrom_mzmlb(file):
    scan_dfs = []
    for spectrum in mzmlb.MzMLb(file):
        if spectrum['ms level'] == 1:
            mz_vals=spectrum['m/z array']
            int_vals = spectrum['intensity array']
            bet_mzs = mz_vals[abs(mz_vals-118.0865)<=0.001]
            bet_ints = int_vals[abs(mz_vals-118.0865)<=0.001]
            rt_val = spectrum['scanList']['scan'][0]['scan start time']
            if(len(bet_mzs)>0):
                df_scan = pd.DataFrame({'mz':bet_mzs, 'int':bet_ints, 'rt':[rt_val]*len(bet_mzs)})
                scan_dfs.append(df_scan)    
    return(pd.concat(scan_dfs, ignore_index=True))
chrom_data = get_chrom_mzmlb('210916_Poo_TruePooAmm-noIS-pos-Full_1.mzMLb')

plt.plot(chrom_data["rt"], chrom_data["int"])
plt.show()