emzed.ms_data¶

`ImmutablePeakMap` ¶

Bases: DbBackedModel

Immutable LCMS experiment wrapper backed by a SQLite database.

`unique_id` `property` ¶

Stable content-based identifier for the peak map.

`chromatogram(mzmin=None, mzmax=None, rtmin=None, rtmax=None, ms_level=None, precursormzmin=None, precursormzmax=None, polarity=None)` ¶

Integrate a chromatogram over the given extraction window.

Parameters:

Name	Description	Default
`mzmin`	minimum fragment m/z included in the chromatogram.	`None`
`mzmax`	maximum fragment m/z included in the chromatogram.	`None`
`rtmin`	minimum retention time in seconds.	`None`
`rtmax`	maximum retention time in seconds.	`None`
`ms_level`	MS level to extract. If omitted, the lowest present level is used.	`None`
`precursormzmin`	minimum precursor m/z for MSn extraction.	`None`
`precursormzmax`	maximum precursor m/z for MSn extraction.	`None`
`polarity`	optional polarity filter, either `"+"` or `"-"`.	`None`

Returns:

Type	Description
	`Chromatogram`.

`close()` ¶

Close the underlying database connection.

`extract(mzmin=None, mzmax=None, rtmin=None, rtmax=None, imin=None, imax=None, mslevelmin=None, mslevelmax=None, precursormzmin=None, precursormzmax=None, polarity=None, *, target_db_file=None)` ¶

Extract a sub-peakmap using RT, m/z, intensity, precursor, and polarity limits.

Parameters:

Name	Description	Default
`mzmin`	minimum fragment m/z to keep.	`None`
`mzmax`	maximum fragment m/z to keep.	`None`
`rtmin`	minimum retention time in seconds.	`None`
`rtmax`	maximum retention time in seconds.	`None`
`imin`	minimum intensity to keep.	`None`
`imax`	maximum intensity to keep.	`None`
`mslevelmin`	minimum MS level to keep.	`None`
`mslevelmax`	maximum MS level to keep.	`None`
`precursormzmin`	minimum precursor m/z to keep for MSn spectra.	`None`
`precursormzmax`	maximum precursor m/z to keep for MSn spectra.	`None`
`polarity`	optional polarity filter, either `"+"` or `"-"`.	`None`
`target_db_file`	optional output database path for the extracted result.	`None`

Returns:

Type	Description
	`PeakMap`.

`extract_for_precursors(mzs, mz_tol, *, target_db_file=None)` ¶

Extract MSn spectra whose precursor windows match the given m/z values.

Parameters:

Name	Description	Default
`mzs`	precursor m/z values to match.	required
`mz_tol`	absolute m/z tolerance used for matching.	required
`target_db_file`	optional output database path for the extracted result.	`None`

Returns:

Type	Description
	`PeakMap`.

`filter(predicate, target_db_file=None)` ¶

Create a new peak map containing spectra that match a predicate.

Parameters:

Name	Type	Description	Default
`predicate`		callable receiving a spectrum and returning `True` for spectra to keep.	required
`target_db_file`		optional output database path for the filtered result.	`None`

Returns:

Type	Description
	`PeakMap`.

`get_dominating_peak_map()` ¶

Return the lowest MS-level sub-peakmap as an MS1-style peak map.

`get_precursors_mzs()` ¶

Return all unique precursor-m/z tuples found in the peak map.

`is_in_memory()` ¶

Return True if the peak map is backed by an in-memory database.

`is_open()` ¶

Return True if the underlying database connection is open.

`load(path, *, target_db_file=None, overwrite=False)` `classmethod` ¶

Load an mzML or mzXML file into an emzed peak-map database.

Parameters:

Name	Description	Default
`path`	source mass-spectrometry file.	required
`target_db_file`	optional output database path. If omitted, an in-memory database is used.	`None`
`overwrite`	overwrite `target_db_file` if it already exists.	`False`

Returns:

Type	Description
	`ImmutablePeakMap`.

`ms_levels()` ¶

Return the MS levels present in the peak map.

`mz_range(ms_level=None)` ¶

Return the m/z range for one MS level or for the full peak map.

Parameters:

Name	Type	Description	Default
`ms_level`		optional MS level. `None` returns the full-range summary.	`None`

`mz_ranges(ms_level=None)` ¶

Return the m/z ranges indexed by MS level.

`open(path)` `classmethod` ¶

Open a peak map database without copying it into memory.

Parameters:

Name	Type	Description	Default
`path`		path to an `emzed` peak-map database file.	required

Returns:

Type	Description
	`ImmutablePeakMap`.

`polarities()` ¶

Return the set of ion polarities present in the peak map.

`representing_mz_peak(mzmin, mzmax, rtmin, rtmax, ms_level=1)` ¶

Return an intensity-weighted representative m/z inside a 2D window.

Parameters:

Name	Description	Default
`mzmin`	minimum m/z bound.	required
`mzmax`	maximum m/z bound.	required
`rtmin`	minimum retention time in seconds.	required
`rtmax`	maximum retention time in seconds.	required
`ms_level`	MS level to inspect.	`1`

Returns:

Type	Description
	representative m/z as `float` or `None` if no peak matches.

`rt_range(ms_level=None)` ¶

Return the retention-time range for one MS level or for the full peak map.

Parameters:

Name	Type	Description	Default
`ms_level`		optional MS level. `None` returns the full-range summary.	`None`

`rt_ranges(ms_level=None)` ¶

Return the retention-time ranges indexed by MS level.

`save(path, *, overwrite=False)` ¶

Write the peak map to mzML or mzXML.

Parameters:

Name	Type	Description	Default
`path`		target output path.	required
`overwrite`		overwrite an existing output file.	`False`

`scan_counts()` ¶

Return the number of scans grouped by MS level.

`split_by_precursors(mz_tol=0.0)` ¶

Split the peak map into sub-peakmaps grouped by precursor m/z tuples.

Parameters:

Name	Type	Description	Default
`mz_tol`		optional binning tolerance used to merge nearly identical precursor tuples.	`0.0`

Returns:

Type	Description
	`dict` mapping precursor tuples to `PeakMap` objects.

`summary()` ¶

Return a compact table summarizing RT, m/z, scan counts, and polarities.

`MSChromatogram` ¶

Mass-spectrometry chromatogram with optional precursor annotation.

`available_types` `property` ¶

Return the list of supported chromatogram type names.

`intensities` `property` ¶

Intensity values of the chromatogram.

`mz` `property` ¶

Target m/z of the chromatogram.

`precursor_mz` `property` ¶

Precursor m/z associated with the chromatogram, if any.

`rts` `property` ¶

Retention times of the chromatogram.

`type` `property` ¶

Return the chromatogram type name.

`rt_range()` ¶

Return the chromatogram retention-time range.

`PeakMap` ¶

Bases: ImmutablePeakMap

Mutable variant of ImmutablePeakMap.

`add_spectrum(spectrum)` ¶

Reject direct mutation on immutable peak maps.

Parameters:

Name	Type	Description	Default
`spectrum`		spectrum that would otherwise be appended.	required

`from_(clz, pm, *, target_db_file=None)` `classmethod` ¶

Copy a peak map into a mutable database-backed instance.

Parameters:

Name	Type	Description	Default
`pm`		source peak map.	required
`target_db_file`		optional target database path for the copy.	`None`

Returns:

Type	Description
	`PeakMap`.

`merge(other)` ¶

Merge another mutable peak map into this one.

Parameters:

Name	Type	Description	Default
`other`		peak map with non-overlapping scan numbers.	required

`spectra_for_modification()` ¶

contextmanager. in this context one can change spectra attributes like rt, ms_level, peaks or polarity

`Spectrum` ¶

Detached in-memory spectrum record.

`unbind()` ¶

dettaches spectrum from peakmap

emzed.ms_data¶

ImmutablePeakMap ¶

unique_id property ¶

chromatogram(mzmin=None, mzmax=None, rtmin=None, rtmax=None, ms_level=None, precursormzmin=None, precursormzmax=None, polarity=None) ¶

close() ¶

extract(mzmin=None, mzmax=None, rtmin=None, rtmax=None, imin=None, imax=None, mslevelmin=None, mslevelmax=None, precursormzmin=None, precursormzmax=None, polarity=None, *, target_db_file=None) ¶

extract_for_precursors(mzs, mz_tol, *, target_db_file=None) ¶

filter(predicate, target_db_file=None) ¶

get_dominating_peak_map() ¶

get_precursors_mzs() ¶

is_in_memory() ¶

is_open() ¶

load(path, *, target_db_file=None, overwrite=False) classmethod ¶

ms_levels() ¶

mz_range(ms_level=None) ¶

mz_ranges(ms_level=None) ¶

open(path) classmethod ¶

polarities() ¶

representing_mz_peak(mzmin, mzmax, rtmin, rtmax, ms_level=1) ¶

rt_range(ms_level=None) ¶

rt_ranges(ms_level=None) ¶

save(path, *, overwrite=False) ¶

scan_counts() ¶

split_by_precursors(mz_tol=0.0) ¶

summary() ¶

MSChromatogram ¶

available_types property ¶

intensities property ¶

mz property ¶

precursor_mz property ¶

rts property ¶

type property ¶

rt_range() ¶

PeakMap ¶

add_spectrum(spectrum) ¶

from_(clz, pm, *, target_db_file=None) classmethod ¶

merge(other) ¶

spectra_for_modification() ¶

Spectrum ¶

unbind() ¶

`ImmutablePeakMap` ¶

`unique_id` `property` ¶

`chromatogram(mzmin=None, mzmax=None, rtmin=None, rtmax=None, ms_level=None, precursormzmin=None, precursormzmax=None, polarity=None)` ¶

`close()` ¶

`extract(mzmin=None, mzmax=None, rtmin=None, rtmax=None, imin=None, imax=None, mslevelmin=None, mslevelmax=None, precursormzmin=None, precursormzmax=None, polarity=None, *, target_db_file=None)` ¶

`extract_for_precursors(mzs, mz_tol, *, target_db_file=None)` ¶

`filter(predicate, target_db_file=None)` ¶

`get_dominating_peak_map()` ¶

`get_precursors_mzs()` ¶

`is_in_memory()` ¶

`is_open()` ¶

`load(path, *, target_db_file=None, overwrite=False)` `classmethod` ¶

`ms_levels()` ¶

`mz_range(ms_level=None)` ¶

`mz_ranges(ms_level=None)` ¶

`open(path)` `classmethod` ¶

`polarities()` ¶

`representing_mz_peak(mzmin, mzmax, rtmin, rtmax, ms_level=1)` ¶

`rt_range(ms_level=None)` ¶

`rt_ranges(ms_level=None)` ¶

`save(path, *, overwrite=False)` ¶

`scan_counts()` ¶

`split_by_precursors(mz_tol=0.0)` ¶

`summary()` ¶

`MSChromatogram` ¶

`available_types` `property` ¶

`intensities` `property` ¶

`mz` `property` ¶

`precursor_mz` `property` ¶

`rts` `property` ¶

`type` `property` ¶

`rt_range()` ¶

`PeakMap` ¶

`add_spectrum(spectrum)` ¶

`from_(clz, pm, *, target_db_file=None)` `classmethod` ¶

`merge(other)` ¶

`spectra_for_modification()` ¶

`Spectrum` ¶

`unbind()` ¶