3.2. Spectrum and Chromatogram
The spectrum class offers a python object for mass spectrometry data.
The spectrum object holds the basic information of the spectrum and offers
methods to interrogate properties of the spectrum.
Data, i.e. mass over charge (m/z) and intensity decoding is performed on demand
and can be accessed via their properties, e.g. peaks
.
The Spectrum class is used in the Reader
class.
There each spectrum is accessible as a spectrum object.
Theoretical spectra can also be created using the setter functions.
For example, m/z values, intensities, and peaks can be set by the
corresponding properties: pymzml.spec.Spectrum.mz
,
pymzml.spec.Spectrum.i
, pymzml.spec.Spectrum.peaks
.
Similar to the spectrum class, the chromatogram class allows interrogation with profile data (time, intensity) in an total ion chromatogram.
3.2.1. Spectrum
- class pymzml.spec.Spectrum(element=<Element ''>, measured_precision=5e-06, *, obo_version=None)[source]
Spectrum class which inherits from class
pymzml.spec.MS_Spectrum
- Parameters:
element (xml.etree.ElementTree.Element) – spectrum as xml element
- Keyword Arguments:
measured_precision (float) – in ppm, i.e. 5e-6 equals to 5 ppm.
- Attributes:
ID
Access the native id (last number in the id attribute) of the spectrum.
TIC
Property to access the total ion current for this spectrum.
- centroidedPeaks
i
Returns the list of the intensity values.
id_dict
Access to all entries stored the id attribute of a spectrum.
index
Access the index of the spectrum.
measured_precision
Sets the measured and internal precision
ms_level
Property to access the ms level.
mz
Returns the list of m/z values.
precursors
List the precursor information of this spectrum, if available.
scan_time
Property to access the retention time and retention time unit.
selected_precursors
Property to access the selected precursors of a MS2 spectrum.
t_mz_set
Creates a set of integers out of transformed m/z values (including all values in the defined imprecision).
transformed_mz_with_error
Returns transformed m/z value with error
transformed_peaks
m/z value is multiplied by the internal precision.
Methods
estimated_noise_level
([mode])Calculates noise threshold for function remove_noise.
extreme_values
(key)Find extreme values, minimal and maximum m/z and intensity
get
(acc[, default])Mimic dicts get function.
get_element_by_name
(name)Get element from the original tree by it's unit name.
get_element_by_path
(hooks)Find elements in spectrum by its path.
Checks if a spectrum has more than one peak for a given m/z value and within the measured precision
has_peak
(mz2find)Checks if a Spectrum has a certain peak.
Function to retrieve the n-highest centroided peaks of the spectrum.
peaks
(peak_type)Decode and return a list of mz/i tuples.
ppm2abs
(value, ppm_value[, direction, factor])Returns the value plus (or minus, dependent on direction) the error (measured precision ) for this value.
reduce
([peak_type, mz_range])Remove all m/z values outside the given range.
remove_noise
([mode, noise_level, ...])Function to remove noise from peaks, centroided peaks and reprofiled peaks.
Property to access the retention time in minutes.
set_peaks
(peaks, peak_type)Assign a custom peak array of type peak_type
similarity_to
(spec2[, round_precision])Compares two spectra and returns cosine
to_string
([encoding, method])Return string representation of the xml element the spectrum was initialized with.
transform_mz
(value)pymzml uses an internal precision for different tasks.
deprecation_warning
estimatedNoiseLevel
extremeValues
get_all_arrays_in_spec
get_array
get_tims_tof_ion_mobility
hasOverlappingPeak
hasPeak
highestPeaks
removeNoise
remove_precursor_peak
similarityTo
transformMZ
- __getitem__(accession)[source]
Access spectrum XML information by tag name
- Parameters:
accession (str) – name of the XML tag
- Returns:
value of the XML tag
- Return type:
value (float or str)
- __add__(other_spec)[source]
Adds two pymzml spectra
- Parameters:
other_spec (Spectrum) – spectrum to add to the current spectrum
- Returns:
reference to the edited spectrum
- Return type:
self (Spectrum)
Example:
>>> import pymzml >>> s = pymzml.spec.Spectrum( measuredPrescision = 20e-6 ) >>> file_to_read = "../mzML_example_files/xy.mzML.gz" >>> run = pymzml.run.Reader( ... file_to_read , ... MS1_Precision = 5e-6 , ... MSn_Precision = 20e-6 ... ) >>> for spec in run: ... s += spec
- __sub__(other_spec)[source]
Subtracts two pymzml spectra.
- Parameters:
other_spec (spec.Spectrum) – spectrum to subtract from the current spectrum
- Returns:
returns self after other_spec was subtracted
- Return type:
self (spec.Spectrum)
- __mul__(value)[source]
Multiplies each intensity with a float, i.e. scales the spectrum.
- Parameters:
value (int, float) – value to multiply the intensities with
- Returns:
- returns self after intensities were scaled
by value
- Return type:
self (spec.Spectrum)
- __truediv__(value)[source]
Divides each intensity by a float, i.e. scales the spectrum.
- Parameters:
value (int, float) – value to divide the intensities by
- Returns:
- returns self after intensities were scaled
by value.
- Return type:
self (spec.Spectrum)
- property ID
Access the native id (last number in the id attribute) of the spectrum.
- Returns:
native ID of the spectrum
- Return type:
ID (str)
- property TIC
Property to access the total ion current for this spectrum.
- Returns:
Total Ion Current of the spectrum.
- Return type:
TIC (float)
- estimated_noise_level(mode='median')[source]
Calculates noise threshold for function remove_noise.
Different modes are available. Default is ‘median’
- Keyword Arguments:
mode (str) – define mode for removing noise. Default = “median” (other modes: “mean”, “mad”)
- Returns:
estimate noise threshold
- Return type:
noise_level (float)
- extreme_values(key)[source]
Find extreme values, minimal and maximum m/z and intensity
- Parameters:
key (str) – m/z : “mz” or intensity : “i”
- Returns:
tuple of minimal and maximum m/z or intensity
- Return type:
extrema (tuple)
- get(acc, default=None)[source]
Mimic dicts get function.
- Parameters:
acc (str) – accession or obo tag to return
default (None, optional) – default value if acc is not found
- has_overlapping_peak(mz)[source]
Checks if a spectrum has more than one peak for a given m/z value and within the measured precision
- Parameters:
mz (float) – m/z value which should be checked
- Returns:
Returns
True
if a nearby peak is detected, otherwiseFalse
- Return type:
Boolean (bool)
- has_peak(mz2find)[source]
Checks if a Spectrum has a certain peak. Requires a m/z value as input and returns a list of peaks if the m/z value is found in the spectrum, otherwise
[]
is returned. Every peak is a tuple of m/z and intensity.Note
Multiple peaks may be found, depending on the defined precisions
- Parameters:
mz2find (float) – m/z value which should be found
- Returns:
list of m/z, i tuples
- Return type:
peaks (list)
Example:
>>> import pymzml >>> example_file = 'tests/data/example.mzML' >>> run = pymzml.run.Reader( ... example_file, ... MS_precisions = { ... 1 : 5e-6, ... 2 : 20e-6 ... } ... ) >>> for spectrum in run: ... if spectrum.ms_level == 2: ... peak_to_find = spectrum.has_peak(1016.5404) ... print(peak_to_find) [(1016.5404, 19141.735187697403)]
- highest_peaks(n)[source]
Function to retrieve the n-highest centroided peaks of the spectrum.
- Parameters:
n (int) – number of highest peaks to return.
- Returns:
list mz, i tupls with n-highest
- Return type:
centroided peaks (list)
Example:
>>> run = pymzml.run.Reader( ... "tests/data/example.mzML.gz", ... MS_precisions = { ... 1 : 5e-6, ... 2 : 20e-6 ... } ... ) >>> for spectrum in run: ... if spectrum.ms_level == 2: ... if spectrum.ID == 1770: ... for mz,i in spectrum.highest_peaks(5): ... print(mz, i)
- property i
Returns the list of the intensity values. If the intensity values are encoded, the function
_decode()
is used to decode the encoded data.The i property can also be set, e.g. for theoretical data. However, it is recommended to use the peaks property to set mz and intensity tuples at same time.
- Returns
i (list): list of intensity values from the analyzed spectrum
- property id_dict
Access to all entries stored the id attribute of a spectrum.
- Returns:
key value pairs for all entries in id attribute of a spectrum
- Return type:
id_dict (dict)
- property index
Access the index of the spectrum.
- Returns:
index of the spectrum
- Return type:
index (int)
Note
This does not necessarily correspond to the native spectrum ID
- property measured_precision
Sets the measured and internal precision
- Returns:
measured precision (e.g. 5e-6)
- Return type:
value (float)
- property ms_level
Property to access the ms level.
- Return type:
ms_level (int)
- property mz
Returns the list of m/z values. If the m/z values are encoded, the function
_decode()
is used to decode the encoded data. The mz property can also be set, e.g. for theoretical data. However, it is recommended to use the peaks property to set mz and intensity tuples at same time.- Returns:
list of m/z values of spectrum.
- Return type:
mz (list)
- peaks(peak_type)[source]
Decode and return a list of mz/i tuples.
- Parameters:
peak_type (str) – currently supported types are: raw, centroided and reprofiled
- Returns:
list or numpy array of mz/i tuples or arrays
- Return type:
peaks (list or ndarray)
- ppm2abs(value, ppm_value, direction=1, factor=1)[source]
Returns the value plus (or minus, dependent on direction) the error (measured precision ) for this value.
- Parameters:
value (float) – m/z value
ppm_value (int) – ppm value
- Keyword Arguments:
direction (int) – plus or minus the considered m/z value. The argument direction should be 1 or -1
factor (int) – multiplication factor for the imprecision. The argument factor should be bigger than 0
- Returns:
imprecision for the given value
- Return type:
imprecision (float)
- property precursors
List the precursor information of this spectrum, if available. :returns: list of precursor ids for this spectrum. :rtype: precursor(list)
- reduce(peak_type='raw', mz_range=(None, None))[source]
Remove all m/z values outside the given range.
- Parameters:
mz_range (tuple) – tuple of min, max values
- Returns:
list of mz, i tuples in the given range.
- Return type:
peaks (list)
- remove_noise(mode='median', noise_level=None, signal_to_noise_threshold=1.0)[source]
Function to remove noise from peaks, centroided peaks and reprofiled peaks.
- Keyword Arguments:
mode (str) – define mode for removing noise. Default = “median”
modes ((other) –
“mean”, “mad”)
noise_level (float): noise threshold signal_to_noise_threshold (float): S/N threshold for a peak to be accepted
- Returns:
Returns a list with tuples of m/z-intensity pairs above the noise threshold
- Return type:
reprofiled peaks (list)
- property scan_time
Property to access the retention time and retention time unit. Please note, that we do not assume the retention time unit, if it is not correctly defined in the mzML. It is set to ‘unicorns’ in this case.
- Returns:
scan_time_unit (str):
- Return type:
scan_time (float)
- scan_time_in_minutes()[source]
Property to access the retention time in minutes. If the retention time unit is defined within the mzML, the retention time is converted into minutes and returned without the unit.
- Return type:
scan_time (float)
- property selected_precursors
Property to access the selected precursors of a MS2 spectrum. Returns a list of dicts containing the precursors mz and, if available intensity and charge for each precursor.
- Return type:
selected_precursors (list)
- set_peaks(peaks, peak_type)[source]
Assign a custom peak array of type peak_type
- Parameters:
peaks (list or ndarray) – list or array of mz/i values
peak_type (str) – Either raw, centroided or reprofiled
- similarity_to(spec2, round_precision=0)[source]
Compares two spectra and returns cosine
- Parameters:
spec2 (Spectrum) – another pymzml spectrum that is compared to the current spectrum.
- Keyword Arguments:
round_precision (int) – precision mzs are rounded to, i.e. round( mz, round_precision )
- Returns:
- value between 0 and 1, i.e. the cosine between the
two spectra.
- Return type:
cosine (float)
Note
Spectra data is transformed into an n-dimensional vector, where m/z values are binned in bins of 10 m/z and the intensities are added up. Then the cosine is calculated between those two vectors. The more similar the specs are, the closer the value is to 1.
- property t_mz_set
Creates a set of integers out of transformed m/z values (including all values in the defined imprecision). This is used to accelerate has_peak function and similar.
- Returns:
set of transformed m/z values
- Return type:
t_mz_set (set)
- transform_mz(value)[source]
pymzml uses an internal precision for different tasks. This precision depends on the measured precision and is calculated when
spec.Spectrum.measured_precision
is invoked. transform_mz can be used to transform m/z values into the internal standard.- Parameters:
value (float) – m/z value
- Returns:
to internal standard transformed mz value this value can be used to probe internal dictionaries, lists or sets, e.g.
pymzml.spec.Spectrum.t_mz_set()
- Return type:
transformed value (float)
Example
>>> import pymzml >>> run = pymzml.run.Reader( ... "test.mzML.gz" , ... MS_precisions = { ... 1 : 5e-6, ... 2 : 20e-6 ... } ... ) >>> >>> for spectrum in run: ... if spectrum.ms_level == 2: ... peak_to_find = spectrum.has_deconvoluted_peak( ... 1044.5804 ... ) ... print(peak_to_find) [(1044.5596, 3809.4356300564586)]
- property transformed_mz_with_error
Returns transformed m/z value with error
- Returns:
Transformed m/z values in dictionary
{
m/z_with_error : [(m/z,intensity), …], …
}
- Return type:
tmz values (dict)
- property transformed_peaks
m/z value is multiplied by the internal precision.
- Returns:
Returns a list of peaks (tuples of mz and intensity). Float m/z values are adjusted by the internal precision to integers.
- Return type:
Transformed peaks (list)
3.2.2. Chromatogram
- class pymzml.spec.Chromatogram(element, measured_precision=5e-06, *, obo_version=None)[source]
Class for Chromatogram access and handling.
- Attributes:
Methods
get_element_by_name
(name)Get element from the original tree by it's unit name.
get_element_by_path
(hooks)Find elements in spectrum by its path.
peaks
()Return the list of peaks of the spectrum as tuples (time, intensity).
to_string
([encoding, method])Return string representation of the xml element the spectrum was initialized with.
- peaks()[source]
Return the list of peaks of the spectrum as tuples (time, intensity).
- Returns:
list of time, intensity tuples
- Return type:
peaks (list)
Example:
>>> import pymzml >>> run = pymzml.run.Reader( ... spectra.mzMl.gz, ... MS_precisions = { ... 1 : 5e-6, ... 2 : 20e-6 ... } ... ) >>> for entry in run: ... if isinstance(entry, pymzml.spec.Chromatogram): ... for time, intensity in entry.peaks: ... print(time, intensity)
Note
The peaks property can also be set, e.g. for theoretical data. It requires a list of time/intensity tuples.
- property profile
Returns the list of peaks of the chromatogram as tuples (time, intensity).
- Returns:
list of time, i tuples
- Return type:
peaks (list)
Example:
>>> import pymzml >>> run = pymzml.run.Reader( ... spectra.mzMl.gz, ... MS_precisions = { ... 1 : 5e-6, ... 2 : 20e-6 ... } ... ) >>> for entry in run: ... if isinstance(entry, pymzml.spec.Chromatogram): ... for time, intensity in entry.peaks: ... print(time, intensity)
Note
The peaks property can also be set, e.g. for theoretical data. It requires a list of time/intensity tuples.
- property time
Returns the list of time values. If the time values are encoded, the function _decode() is used to decode the encoded data.
The time property can also be set, e.g. for theoretical data. However, it is recommended to use the profile property to set time and intensity tuples at same time.
- Returns:
list of time values from the analyzed chromatogram
- Return type:
time (list)
3.2.3. MS_Spectrum
- class pymzml.spec.MS_Spectrum[source]
General spectrum class for data handling.
- Attributes:
measured_precision
Set the measured and internal precision.
Methods
get_element_by_name
(name)Get element from the original tree by it's unit name.
get_element_by_path
(hooks)Find elements in spectrum by its path.
to_string
([encoding, method])Return string representation of the xml element the spectrum was initialized with.
- get_element_by_name(name)[source]
Get element from the original tree by it’s unit name.
- Parameters:
name (str) – unit name of the mzml element.
- Keyword Arguments:
obo_version (str, optional) – obo version number.
- get_element_by_path(hooks)[source]
Find elements in spectrum by its path.
- Parameters:
hooks (list) – list of parent elements for the target element.
- Returns:
list of XML objects found in the path
- Return type:
elements (list)
Example
To access cvParam in scanWindow tag:
>>> spec.get_element_by_path(['scanList', 'scan', 'scanWindowList', ... 'scanWindow', 'cvParam'])
- property measured_precision
Set the measured and internal precision.
- Returns:
measured Precision (e.g. 5e-6)
- Return type:
value (float)
- to_string(encoding='latin-1', method='xml')[source]
Return string representation of the xml element the spectrum was initialized with.
- Keyword Arguments:
encoding (str) –
text encoding of the returned string.
Default is latin-1.
method (str) –
text format of the returned string.
Default is xml, alternatives are html and text.
- Returns:
xml string representation of the spectrum.
- Return type:
element (str)