figure1：reading .raw data

[Landau1994]

The original code may be wrong, According to my test, this is the correct version:

def load_thermo_raw(
    raw_file,
    most_abundant=1000
):
    """
    Load a Thermo raw file and extract all spectra
    """
    #from pyrawfilereader import RawFileReader
    
    rawfile = RawFileReader(raw_file)

    spec_indices = np.array(
        range(rawfile.FirstSpectrumNumber, rawfile.LastSpectrumNumber + 1)
    )

    scan_list = []
    rt_list = []
    mass_list = []
    int_list = []
    ms_list = []
    prec_mzs_list = []
    mono_mzs_list = []
    charge_list = []

    for i in tqdm((spec_indices)):
        i = int(i)
        try:
            ms_order = rawfile.GetMSOrderForScanNum(i).value__
            rt = rawfile.RTFromScanNum(i)
            

            if ms_order == 2:
                prec_mz = rawfile.GetPrecursorMassForScanNum(i, 0)

                mono_mz, charge = rawfile.GetMS2MonoMzAndChargeFromScanNum(i)
            else:
                prec_mz, mono_mz, charge = 0,0,0

            masses, intensity = rawfile.GetCentroidMassListFromScanNum(i)
            if ms_order == 2:
                masses, intensity = get_most_abundant(masses, intensity, most_abundant)

            scan_list.append(i)
            rt_list.append(rt)
            mass_list.append(np.array(masses))
            int_list.append(np.array(intensity, dtype=np.int64))
            ms_list.append(ms_order)
            prec_mzs_list.append(prec_mz)
            mono_mzs_list.append(mono_mz)
            charge_list.append(charge)
        except KeyboardInterrupt as e:
            raise e
        except SystemExit as e:
            raise e
        except Exception as e:
            logging.info(f"Bad scan={i} in raw file '{raw_file}'")

    scan_list_ms1 = [scan_list[i] for i, _ in enumerate(ms_list) if _ == 1]
    rt_list_ms1 = [rt_list[i] for i, _ in enumerate(ms_list) if _ == 1]
    mass_list_ms1 = [mass_list[i] for i, _ in enumerate(ms_list) if _ == 1]
    int_list_ms1 = [int_list[i] for i, _ in enumerate(ms_list) if _ == 1]
    ms_list_ms1 = [ms_list[i] for i, _ in enumerate(ms_list) if _ == 1]

    scan_list_ms2 = [scan_list[i] for i, _ in enumerate(ms_list) if _ == 2]
    rt_list_ms2 = [rt_list[i] for i, _ in enumerate(ms_list) if _ == 2]
    mass_list_ms2 = [mass_list[i] for i, _ in enumerate(ms_list) if _ == 2]
    int_list_ms2 = [int_list[i] for i, _ in enumerate(ms_list) if _ == 2]
    ms_list_ms2 = [ms_list[i] for i, _ in enumerate(ms_list) if _ == 2]
    mono_mzs2 = [mono_mzs_list[i] for i, _ in enumerate(ms_list) if _ == 2]
    charge2 = [charge_list[i] for i, _ in enumerate(ms_list) if _ == 2]

    prec_mass_list2 = [
        calculate_mass(mono_mzs_list[i], charge_list[i])
        for i, _ in enumerate(ms_list)
        if _ == 2
    ]

    check_sanity(mass_list)

    data = {}
    
    data["scan_list_ms1"] = np.array(scan_list_ms1)
    data["rt_list_ms1"] = np.array(rt_list_ms1)
    data["mass_list_ms1"] = np.array(mass_list_ms1, dtype=object)
    data["int_list_ms1"] = np.array(int_list_ms1, dtype=object)
    data["ms_list_ms1"] = np.array(ms_list_ms1)

    data["scan_list_ms2"] = np.array(scan_list_ms2)
    data["rt_list_ms2"] = np.array(rt_list_ms2)
    data["mass_list_ms2"] = mass_list_ms2
    data["int_list_ms2"] = int_list_ms2
    data["ms_list_ms2"] = np.array(ms_list_ms2)
    data["prec_mass_list2"] = np.array(prec_mass_list2)
    data["mono_mzs2"] = np.array(mono_mzs2)
    data["charge_ms2"] = np.array(charge2)
    
    rawfile.Close()
    return data