tidyms.MSSpectrum

class MSSpectrum(mz: ndarray, spint: ndarray, time: float | None = None, ms_level: int = 1, polarity: int | None = None, instrument: str = 'qtof', is_centroid: bool = True)

Representation of a Mass Spectrum. Manages conversion to centroid and plotting of data.

Attributes:

mzarray

m/z data

spintarray

Intensity data

timefloat or None

Time at which the spectrum was acquired

ms_levelint

MS level of the scan

polarityint or None

Polarity used to acquire the data.

instrument{“qtof”, “orbitrap”}, default=”qtof”

MS instrument type. Used to set default values in methods.

is_centroidbool

True if the data is in centroid mode.

find_centroids(min_snr: float = 10.0, min_distance: float | None = None) → Tuple[ndarray, ndarray]

Find centroids in the spectrum.

Parameters:

min_snrpositive number, default=10.0

Minimum signal-to-noise ratio of the peaks.

min_distancepositive number or None, default=None

Minimum distance between consecutive peaks. If None, the value is set to 0.01 if self.instrument is "qtof" or to 0.005 if self.instrument is "orbitrap".

Returns:

centroidarray

m/z centroids. If self.is_centroid is True, returns self.mz.

areaarray

peak area. If self.is_centroid is True, returns self.spint.

plot(fig_params: dict | None = None, line_params: dict | None = None, show: bool = True) → figure

Plot the spectrum using Bokeh.

Parameters:

fig_paramsdict or None, default=None

key-value parameters to pass to bokeh.plotting.figure.

line_paramsdict, or None, default=None

key-value parameters to pass to bokeh.plotting.figure.line.

showbool, default=True

If True calls bokeh.plotting.show on the Figure.

Returns:

bokeh.plotting.figure