def read_scans(mzml_file, ms_levels=(1, 2), should_renumber_ifmissing=True):
"""
yields all spectra from an mzML file with level in ms_levels, or
all processable scans if ms_levels not specified
:param mzml_file:
:param ms_levels:
:param min_pprophet:
:param should_renumber_ifmissing: If this is true and we're unable to get integer
scan numbers from the spactra, renumber them from 1 to N. If false, fail if we
can't parse an integer from the scan number field
:return:
"""
with mzml.MzML(mzml_file) as reader:
cur_scanidx_1based = 0
for scan in reader:
cur_scanidx_1based += 1
if scan['ms level'] in ms_levels:
# ignore this scan if we get a ValueError.
# ValueError is only raised if we can't infer charge.
# If we still have enough scans where we could infer charge, OK to
# ignore these.
try:
yield read_scan(scan,
default_scan_number=cur_scanidx_1based
if should_renumber_ifmissing else None)
except ValueError as e:
logger.debug("Warning! Failed to read scan: %s" % e)
def readmzXML(file_paths):
data_dict = {}
for file_path in file_paths:
data = mzml.MzML(file_path)
file_num = len(data)
for spectrum in data:
data_dict[spectrum['spectrum title']] = {'m/z':spectrum['m/z array'],'intensity':spectrum['intensity array']}
print('successfully loaded '+str(file_num)+' raw spectra from'+file_path)
return data_dict
def get_spectra(source: Union[IO, str], scan_nrs: Sequence[int] = None)\
-> Iterator[MsmsSpectrum]:
"""
Get the MS/MS spectra from the given mzML file, optionally filtering by
scan number.
Parameters
----------
source : Union[IO, str]
The mzML source (file name or open file object) from which the spectra
are read.
scan_nrs : Sequence[int]
Only read spectra with the given scan numbers. If `None`, no filtering
on scan number is performed.
Returns
-------
Iterator[MsmsSpectrum]
An iterator over the requested spectra in the given file.
"""
with mzml.MzML(source) as f_in:
# Iterate over a subset of spectra filtered by scan number.
if scan_nrs is not None:
def spectrum_it():
for scan_nr in scan_nrs:
yield f_in.get_by_id(
f'controllerType=0 controllerNumber=1 scan={scan_nr}')
# Or iterate over all MS/MS spectra.
else:
def spectrum_it():
for spectrum_dict in f_in:
if int(spectrum_dict.get('ms level', -1)) == 2:
yield spectrum_dict
try:
for spectrum in spectrum_it():
try:
yield _parse_spectrum(spectrum)
except ValueError as e:
pass
# logger.warning(f'Failed to read spectrum %s: %s',
# spectrum['id'], e)
except LxmlError as e:
logger.warning('Failed to read file %s: %s', source, e)
def extract_from_mzml(path):
# Extract the data from the mzml, if we havnt already
if not os.path.exists(f'{path}mzML.json'):
if not multiprocessing:
print(
'Extracting data from mzML ',
end='\r')
data = mzml.MzML(f'{path}file.mzML')
# Extracted data
extracted = {'ms1': {}, 'ms2': {}}
# Extract the necessary data from spectra
for spectrum in data:
if spectrum['ms level'] == 1:
# Scan id
scan_id = int(spectrum['id'].split('scan=')[1])
# Deal with ms level 1 spectra
ms1_spectrum = process_ms1(spectrum)
extracted['ms1'][scan_id] = {
'mz': ms1_spectrum['mz'],
'intensity': ms1_spectrum['intensity'],
'scan_time': ms1_spectrum['scan_time']
}
elif spectrum['ms level'] == 2:
# Scan id
scan_id = int(spectrum['id'].split('scan=')[1])
# Deal with ms level 1 spectra
ms2_spectrum = process_ms2(spectrum)
extracted['ms2'][scan_id] = {
'scan_index': ms2_spectrum['scan_index'],
'precursor_scan': ms2_spectrum['precursor_scan'],
'precursor_ion': ms2_spectrum['precursor_ion'],
'm/z_array': [mz for mz in ms2_spectrum['m/z']],
'rt_array': [rt for rt in ms2_spectrum['rt']]
}
else:
pass
with gzip.GzipFile(f'{path}mzML.json', 'w') as fout:
fout.write(json.dumps(extracted).encode('utf-8'))
fout.close()
def mzml_to_pandas_df(filename):
"""
Reads mzML file and returns a pandas.DataFrame.
"""
cols = ["retentionTime", "m/z array", "intensity array"]
slices = []
file = mzml.MzML(filename)
while True:
try:
data = file.next()
data["retentionTime"] = data["scanList"]["scan"][0]["scan time"] / 60
del data["scanList"]
slices.append(pd.DataFrame(data))
except:
break
df = pd.concat(slices)[cols]
df_to_numeric(df)
return df
def mzml_to_pandas_df(filename):
'''
Reads mzML file and returns a pandas.DataFrame.
'''
cols = ['retentionTime', 'm/z array', 'intensity array']
slices = []
file = mzml.MzML(filename)
while True:
try:
data = file.next()
data['retentionTime'] = data['scanList']['scan'][0][
'scan time'] / 60
del data['scanList']
slices.append(pd.DataFrame(data))
except:
break
df = pd.concat(slices)[cols]
df_to_numeric(df)
return df
def mzml_to_pandas_df_pyteomics(fn):
'''
Reads mzML file and returns a pandas.DataFrame.
'''
cols = ['retentionTime', 'm/z array', 'intensity array']
slices = []
with mzml.MzML(fn) as ms_data:
while True:
try:
data = ms_data.next()
data['retentionTime'] = data['scanList']['scan'][0][
'scan time'] / 60
del data['scanList']
slices.append(pd.DataFrame(data))
except:
break
df = pd.concat(slices)[cols]
df_to_numeric(df)
df['intensity array'] = df['intensity array'].astype(int)
df = df.reset_index(drop=True)
return df
def internalmzML(path):
# Extract the data from the mzml, if we havnt already
if not os.path.exists(f'{path}mzML.json'):
if not multithread:
print(
'Extracting data from mzML ',
end='\r')
data = mzml.MzML(f'{path}file.mzML')
# Extracted data
extracted = {'ms1': {}} # , 'ms2': {}}
# Extract the necessary data from spectra
for spectrum in data:
if spectrum['ms level'] == 1:
# Scan id
scan_id = int(spectrum['id'].split('scan=')[1])
# Deal with ms level 1 spectra
ms1_spectrum = process_ms1(spectrum)
extracted['ms1'][scan_id] = {
'mz': ms1_spectrum['mz'],
'intensity': ms1_spectrum['intensity'],
'scan_time': ms1_spectrum['scan_time']
}
else:
pass
# elif spectrum['ms level'] == 2:
# # Scan id
# scan_id = int(spectrum['id'].split('scan=')[1])
#
# # Deal with ms level 1 spectra
# ms1_spectrum = process_ms1(spectrum)
# extracted['ms1'][scan_id] = {'mz': process_ms2['precursor_scan'],
# 'intensity': process_ms2['precursor_ion'],
# 'scan_time': process_ms2['scan_index']}
with gzip.GzipFile(f'{path}mzML.json', 'w') as fout:
fout.write(json.dumps(extracted).encode('utf-8'))
fout.close()
os.remove(f'{path}file.mzML')
def read(mzml_file: str, max_peaks: int = None, min_intensity: float = None)\
-> Tuple[np.ndarray, DIAScan]:
"""
Read an mzML file from a DIA experiment.
Parameters
----------
mzml_file : str
The mzML file to read.
Returns
-------
diadem.dataset.DIARun
A DIARun object containg the raw data.
"""
kwargs = {"max_peaks": max_peaks, "min_intensity": min_intensity}
with mzml.MzML(mzml_file) as mz_dat:
scans = DIARun([
s for s in _pbar(mz_dat.map(_mkscan, kwargs=kwargs, processes=4))
])
return scans
def qc1_main():
argparser = ArgumentParser(description="iRT peptide QC tool")
argparser.add_argument('--mzml', type=str, required=True, help="MzML file")
argparser.add_argument('--targets',
type=str,
required=True,
help="Targets file")
argparser.add_argument('--ms1-ppm',
type=float,
default=5,
help="MS1 extraction window in ppm")
argparser.add_argument('--ms2-prec-tolerance',
type=float,
default=0.01,
help="MS2 precursor tolerance")
argparser.add_argument('--ms2-frag-tolerance',
type=float,
default=1,
help="MS2 precursor tolerance")
argparser.add_argument('--width-1-pc',
type=float,
default=50,
help="Chromatographic width 1 in %% of apex")
argparser.add_argument('--width-2-pc',
type=float,
default=5,
help="Chromatographic width 2 in %% of apex")
argparser.add_argument('--debug',
action="store_true",
help="Pickle cache input file")
argparser = argparser.parse_args()
b_fname = ".".join(argparser.mzml.split(".")[:-1])
pdf = PdfPages(b_fname + "_Figs.pdf")
if argparser.debug:
import pickle
import time
import os
if os.path.exists(argparser.mzml + ".pkl"):
with open(argparser.mzml + ".pkl", "rb") as f_:
_start_time = time.time()
print("Unpickling")
exp = lcmsms.LCMSMSExperiment(
tqdm.tqdm(pickle.load(f_)),
prec_tolerance=argparser.ms2_prec_tolerance)
print(f"Unpickled in {time.time()-_start_time} seconds")
else:
print("Reading and pickling")
mzml_ = list(tqdm.tqdm(mzml.MzML(argparser.mzml)))
with open(argparser.mzml + ".pkl", "wb") as f_:
pickle.dump(mzml_, f_)
print("Pickled, parsing experiment")
exp = lcmsms.LCMSMSExperiment(
tqdm.tqdm(mzml_), prec_tolerance=argparser.ms2_prec_tolerance)
del mzml_
else:
exp = lcmsms.LCMSMSExperiment(
tqdm.tqdm(mzml.MzML(argparser.mzml)),
prec_tolerance=argparser.ms2_prec_tolerance)
### MS1 processing ####
targets = pd.read_csv(argparser.targets, sep='\t')
targets_ms1 = targets[["Sequence", "Precursor_Mz"]].drop_duplicates()
results_ms1 = pd.DataFrame(columns=[
"Sequence",
"Precursor_Mz",
"Apex_time",
f"Width_{argparser.width_1_pc}_pc_time_start",
f"Width_{argparser.width_1_pc}_pc_time_end",
f"Width_{argparser.width_1_pc}_xic_area",
f"Width_{argparser.width_2_pc}_pc_time_start",
f"Width_{argparser.width_2_pc}_pc_time_end",
f"Width_{argparser.width_2_pc}_xic_area",
f"MS1_mass_apex_mz",
f"MS1_apex_height",
f"MS1_peak_halfwidth",
f"MS1_peak_area",
f"TIC_MS2",
])
#from matplotlib.backends.backend_pdf import PdfPages
#pdf = PdfPages('MS1.pdf')
fig, axs = plt.subplots(len(targets_ms1),
4,
figsize=(15, 60),
gridspec_kw={'width_ratios': [1, 1, 1, 1]})
plt.subplots_adjust(hspace=0.5)
n = 0
for k, row in targets_ms1.iterrows():
mz = row["Precursor_Mz"]
seq = row["Sequence"]
ch = exp.ms1.xic(mz, argparser.ms1_ppm)
chs = ch.smooth(sigma=2)
apext, apexi = ch.get_apex()
width1 = chs.get_width_pc(argparser.width_1_pc)
width2 = chs.get_width_pc(argparser.width_2_pc)
area1 = chs.get_width_pc_area(argparser.width_1_pc)
area2 = chs.get_width_pc_area(argparser.width_2_pc)
spec = exp.ms1[apext]
ms1_apex_mz, ms1_apex_int = spec.get_apex_around(mz, 0.05)
ms1_hw = spec.get_apex_width_pc(mz, apex_pc=50, tolerance=0.05)
ms1_area = spec.get_peak_area(mz, tolerance=0.05)
### PLOTS ###
# XIC
axs[n, 0].ticklabel_format(axis="y", style='sci', scilimits=(0, 0))
axs[n, 0].ticklabel_format(axis="x", style='plain')
axs[n, 0].plot(ch.t, ch.i, "g-")
#axs[n, 0].plot(xictimes, xic)
#axs[n, 0].plot(xictimes, asym_peak(xictimes, *popt), 'r-')
axs[n, 0].vlines(apext, 0, apexi * 1.1)
axs[n, 0].title.set_text(f"{seq}\nmz={mz:.4f}\napex@{apext:.2f}min")
axs[n, 0].set_xlim(15, 30)
# XIC zoom
axs[n, 1].ticklabel_format(axis="y", style='sci', scilimits=(0, 0))
axs[n, 1].ticklabel_format(axis="x", style='plain')
axs[n, 1].plot(ch.t, ch.i, "gx-")
axs[n, 1].plot(chs.t, chs.i, "rx-")
#axs[n, 1].plot(xictimes, asym_peak(xictimes, *popt), 'r-')
axs[n, 1].vlines(apext, 0, apexi)
axs[n, 1].title.set_text(f"MS1 XIC zoon\n mz={mz:.4f}")
axs[n, 1].hlines(apexi * 0.5, *width1)
axs[n, 1].hlines(apexi * 0.05, *width2)
axs[n, 1].set_xlim(apext - 0.2, apext + 0.4)
axs[n, 1].text(0.45,
0.95,
f"Area50={area1:.3e}\nArea5 ={area2:.3e}",
transform=axs[n, 1].transAxes,
fontsize=10,
verticalalignment='top')
# MS1 spectrum
spec = exp.ms1[apext]
axs[n, 2].ticklabel_format(axis="y", style='sci', scilimits=(0, 0))
axs[n, 2].ticklabel_format(axis="x", style='plain')
axs[n, 2].title.set_text(f"MS1 spectrum\n@time={apext:.2f}min")
spec.plot(ax=axs[n, 2], marks=[ms1_apex_mz])
# MS1 spectrum zoom
ms1_tolerance = ms1_apex_mz * argparser.ms1_ppm * 1e-6
spec_zoom = spec[ms1_apex_mz -
argparser.ms2_prec_tolerance:ms1_apex_mz +
argparser.ms2_prec_tolerance] # No /2 (sic!)
axs[n, 3].ticklabel_format(axis="y", style='sci', scilimits=(0, 0))
axs[n, 3].ticklabel_format(axis="x",
style='sci',
scilimits=(-3, -3),
useOffset=ms1_apex_mz)
#axs[n, 3].xaxis.set_major_formatter(FormatStrFormatter('%.2f'))
spec_zoom.plot("go-", ax=axs[n, 3])
axs[n, 3].title.set_text("MS1 zoom\n mz={:.4f}".format(mz))
axs[n, 3].vlines(ms1_apex_mz, 0, ms1_apex_int, "r")
ms1_w_left, ms1_w_right = spec.get_apex_times_pc(ms1_apex_mz,
apex_pc=50,
tolerance=0.05)
axs[n, 3].hlines(ms1_apex_int / 2, ms1_w_left, ms1_w_right, "r")
axs[n, 3].text(0.55,
0.95,
f"Area={ms1_area:.2e}\nHW={ms1_hw:.2e}",
transform=axs[n, 3].transAxes,
fontsize=10,
verticalalignment='top')
n += 1
############
row['Apex_time'] = apext
row[f"Width_{argparser.width_1_pc}_pc_time_start"] = width1[0]
row[f"Width_{argparser.width_1_pc}_pc_time_end"] = width1[1]
row[f"Width_{argparser.width_1_pc}_xic_area"] = area1
row[f"Width_{argparser.width_2_pc}_pc_time_start"] = width2[0]
row[f"Width_{argparser.width_2_pc}_pc_time_end"] = width2[1]
row[f"Width_{argparser.width_2_pc}_xic_area"] = area2
row[f"MS1_mass_apex_mz"] = ms1_apex_mz
row[f"MS1_apex_height"] = ms1_apex_int
row[f"MS1_peak_halfwidth"] = ms1_hw
row[f"MS1_peak_area"] = ms1_area
results_ms1 = results_ms1.append(row)
pdf.savefig(fig)
plt.close(fig)
### MS2 processing ###
results_ms1.set_index("Sequence", drop=True, inplace=True)
targets_ms2 = targets[["Sequence", "Precursor_Mz",
"Product_Mz"]].drop_duplicates()
results_ms2 = pd.DataFrame(columns=[
"Sequence",
"Precursor_Mz",
"Product_Mz",
"MS2_TIC_Apex_time",
"MS2_mass_apex_mz",
"MS2_apex_height",
"MS2_peak_halfwidth",
"MS2_peak_area",
])
n_ = max(
map(lambda x: len(x[1]),
targets_ms2.groupby(by=["Sequence", "Precursor_Mz"])))
fig, axs = plt.subplots(len(targets_ms1), 3 + n_, figsize=(15, 100))
plt.subplots_adjust(hspace=0.5)
plt.subplots_adjust(hspace=0.5)
n = -1
for k, grp in targets_ms2.groupby(by=["Sequence", "Precursor_Mz"]):
n += 1
seq = k[0]
prec = k[1]
apext = results_ms1.loc[seq, "Apex_time"]
start = results_ms1.loc[seq,
f"Width_{argparser.width_2_pc}_pc_time_start"]
stop = results_ms1.loc[seq,
f"Width_{argparser.width_2_pc}_pc_time_end"]
ms2_all = exp.ms2.extract(prec)
ms2_ext = ms2_all[start - argparser.ms2_frag_tolerance / 2:stop +
argparser.ms2_frag_tolerance / 2]
#spec = ms2_ext[apext]
tic_apext, tic_apexint = ms2_ext.tic.get_apex()
results_ms1.loc[seq, "TIC_MS2"] = tic_apexint
spec = ms2_ext[tic_apext]
### PLOTS ###
# TIC MS2
axs[n, 0].ticklabel_format(axis="y", style='sci', scilimits=(0, 0))
axs[n, 0].ticklabel_format(axis="x", style='plain')
axs[n, 0].plot(ms2_all.tic.t, ms2_all.tic.i, "g-")
axs[n, 0].title.set_text("TIC MS2\nmz={:.4f}\n apex@{:.2f}\n".format(
prec, tic_apext))
# TIC MS2 zoom
axs[n, 1].ticklabel_format(axis="y", style='sci', scilimits=(0, 0))
axs[n, 1].ticklabel_format(axis="x", style='plain')
axs[n, 1].plot(ms2_ext.tic.t, ms2_ext.tic.i, "g-")
axs[n, 1].vlines(tic_apext, 0, tic_apexint, "r")
axs[n, 1].title.set_text(
f"TIC MS2 zoom\nmz={prec:.4f}\n apex@{tic_apext:.2f}\n")
# MS2 spectrum
axs[n, 2].ticklabel_format(axis="y", style='sci', scilimits=(0, 0))
axs[n, 2].ticklabel_format(axis="x", style='plain')
spec.plot(ax=axs[n, 2])
axs[n, 2].title.set_text(
f"MS/MS for\n{prec:.4f}\n@time={tic_apext:.2f}min\n")
nn = 3
for kk, row in grp.iterrows():
frag = row["Product_Mz"]
try:
fmz, fint = spec.get_apex_around(frag,
argparser.ms2_frag_tolerance)
f_hw = spec.get_apex_width_pc(
frag, apex_pc=50, tolerance=argparser.ms2_frag_tolerance)
f_area = spec.get_peak_area(
fmz, tolerance=argparser.ms2_frag_tolerance)
s_ext = spec[fmz - argparser.ms2_frag_tolerance / 2:fmz +
argparser.ms2_frag_tolerance / 2]
s_ext.plot("go-", ax=axs[n, nn])
axs[n, nn].ticklabel_format(axis="y",
style='sci',
scilimits=(0, 0))
#axs[n, nn].ticklabel_format(axis="x", style='sci', scilimits=(-2,-2), useOffset=fmz)
axs[n, nn].ticklabel_format(axis="x", style='plain')
axs[n, nn].title.set_text(f"MS2 zoom\nmz={fmz:.4f}\n")
axs[n, nn].vlines(fmz, 0, max(s_ext.i), "r")
axs[n, nn].vlines(frag, 0, max(s_ext.i), "blue")
axs[n, 2].plot([frag], [fint], "rx") #, markersize=15)
ms2_w_left, ms2_w_right = s_ext.get_apex_times_pc(
fmz, apex_pc=50, tolerance=0.05)
axs[n, nn].hlines(fint / 2, ms2_w_left, ms2_w_right, "r")
axs[n, nn].text(0.6,
0.98,
f"Area=\n{ms1_area:.2e}\n\nHW=\n{ms1_hw:.2e}",
transform=axs[n, nn].transAxes,
fontsize=8,
verticalalignment='top')
except lcmsms.PeaksNotFound:
print(f"No MS2 peak for {prec:.4f}/{frag:.4f}")
f_hw = 0
f_area = 0
fmz = 0
fint = 0
nn += 1
row["MS2_TIC_Apex_time"] = tic_apext
row["MS2_mass_apex_mz"] = fmz
row["MS2_apex_height"] = fint
row["MS2_peak_halfwidth"] = f_hw
row["MS2_peak_area"] = f_area
results_ms2 = results_ms2.append(row)
pdf.savefig(fig)
plt.close(fig)
results_ms2.set_index("Sequence", drop=True, inplace=True)
fig.savefig("MS1.pdf", dpi=1200, format='pdf', bbox_inches='tight')
ms1_fname = b_fname + "_MS1_table.csv"
ms2_fname = b_fname + "_MS2_table.csv"
results_ms1.to_csv(ms1_fname, sep='\t')
results_ms2.to_csv(ms2_fname, sep='\t')
pdf.close()
mzid_df = pd.DataFrame({'file': file_location, 'id': spectrum_ids, 'seq': seq})
def _parse_mzml_entry(entry):
ID = str(entry['id'])
mz = np.array(entry['m/z array'])
intensities = np.array(entry['intensity array'])
return ID, mz, intensities
all_spectra = []
for file in np.unique(file_location):
print(file)
indexed = mzml.MzML(file)
for i, entry in enumerate(indexed.map(_parse_mzml_entry)):
tupl = (file, ) + entry
all_spectra.append(tupl)
mzml_location, ids, mz, intensities = zip(*all_spectra)
spectra_df = pd.DataFrame({
'file': mzml_location,
'id': ids,
'mz': mz,
'intensities': intensities
})
#### MERGE: mzid + mzml
import numpy as np
import pandas as pd
# %%
# define parsing function
def _parse_mzml_entry(entry):
ID = str(entry['id'])
mz = np.array(entry['m/z array'])
intensities = np.array(entry['intensity array'])
return ID, mz, intensities
all_spectra = []
data = '/home/ubuntu/data/jiahao/trp/output/Run1_U4_2000ng.mzML'
file = mzml.MzML(data)
for i, entry in enumerate(file.map(_parse_mzml_entry)):
tupl = (data, ) + entry
all_spectra.append(tupl)
# %%
# generate pandas dataframe
mzml_location, ids, mz, intensities = zip(*all_spectra)
spectra_df = pd.DataFrame({
'file': mzml_location,
'id': ids,
'mz': mz,
'intensities': intensities
})
