ms_deisotope documentation
Index
Contents
Index
Symbols
|
_
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A
|
B
|
C
|
D
|
E
|
F
|
G
|
H
|
I
|
L
|
M
|
mgf
|
M
|
mzml
|
M
|
N
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nativeID
|
N
|
O
|
P
|
Q
|
R
|
S
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scan_id
|
scan_index
|
S
|
T
|
U
|
V
|
W
Symbols
--averagine <averagine>
ms-deisotope command line option
--background-reduction <float>
ms-deisotope command line option
--cache-size <int>
ms-index-spectrum-clustering command line option
--compress
ms-index-mgf command line option
ms-index-mzml command line option
--compression <choice>
ms-index-mzmlb command line option
--correct-precursor-mz
ms-index-mzml command line option
ms-index-mzmlb command line option
--deconvoluted
ms-index-metadata-index command line option
ms-index-spectrum-clustering command line option
--default-precursor-ion-selection-window <float>
ms-deisotope command line option
--diagnostics
ms-index-describe command line option
--end-time <float>
ms-deisotope command line option
--extract-only-tandem-envelopes
ms-deisotope command line option
--ignore-msn
ms-deisotope command line option
--in-memory
ms-index-spectrum-clustering command line option
--isotopic-strictness <float>
ms-deisotope command line option
--mass-offset <float>
ms-deisotope command line option
--maximum-charge <int>
ms-deisotope command line option
--missed-peaks <int>
ms-deisotope command line option
--ms1-averaging <int>
ms-deisotope command line option
--ms1-filter <func>
ms-index-mzml command line option
ms-index-mzmlb command line option
--msn-averagine <averagine>
ms-deisotope command line option
--msn-background-reduction <float>
ms-deisotope command line option
--msn-filter <func>
ms-index-mgf command line option
ms-index-mzml command line option
ms-index-mzmlb command line option
--msn-isotopic-strictness <float>
ms-deisotope command line option
--msn-missed-peaks <int>
ms-deisotope command line option
--msn-score-threshold <float>
ms-deisotope command line option
--msn-transform <func>
ms-deisotope command line option
--name <string>
ms-deisotope command line option
--no-update-metadata
ms-index-mzml command line option
ms-index-mzmlb command line option
--option <tuple>
ms-index-mzml command line option
ms-index-mzmlb command line option
--output <path>
ms-index-msms-intervals command line option
ms-index-spectrum-clustering command line option
--pick-peaks
ms-index-mzml command line option
ms-index-mzmlb command line option
--precursor-error-tolerance <float>
ms-index-spectrum-clustering command line option
--processes <int>
ms-deisotope command line option
ms-index-metadata-index command line option
ms-index-msms-intervals command line option
--reprofile
ms-index-mzml command line option
ms-index-mzmlb command line option
--score-threshold <float>
ms-deisotope command line option
--signal-to-noise-threshold <float>
ms-deisotope command line option
--similarity-threshold <float>
ms-index-spectrum-clustering command line option
--start-time <float>
ms-deisotope command line option
--transform <func>
ms-deisotope command line option
--update-metadata
ms-index-mzml command line option
ms-index-mzmlb command line option
--verbose
ms-deisotope command line option
-a
ms-deisotope command line option
-an
ms-deisotope command line option
-b
ms-deisotope command line option
-bn
ms-deisotope command line option
-c
ms-deisotope command line option
ms-index-mzml command line option
ms-index-mzmlb command line option
ms-index-spectrum-clustering command line option
-D
ms-deisotope command line option
ms-index-metadata-index command line option
ms-index-spectrum-clustering command line option
-d
ms-index-describe command line option
-e
ms-deisotope command line option
-f
ms-index-mzml command line option
ms-index-mzmlb command line option
-g
ms-deisotope command line option
-i
ms-deisotope command line option
-in
ms-deisotope command line option
-M
ms-index-spectrum-clustering command line option
-m
ms-deisotope command line option
ms-index-spectrum-clustering command line option
-mn
ms-deisotope command line option
-mo
ms-deisotope command line option
-n
ms-deisotope command line option
-o
ms-index-msms-intervals command line option
ms-index-spectrum-clustering command line option
-p
ms-deisotope command line option
ms-index-metadata-index command line option
ms-index-msms-intervals command line option
ms-index-mzml command line option
ms-index-mzmlb command line option
-r
ms-deisotope command line option
ms-index-mzml command line option
ms-index-mzmlb command line option
-rn
ms-deisotope command line option
ms-index-mgf command line option
ms-index-mzml command line option
ms-index-mzmlb command line option
-s
ms-deisotope command line option
-snr
ms-deisotope command line option
-t
ms-deisotope command line option
ms-index-spectrum-clustering command line option
-tn
ms-deisotope command line option
-v
ms-deisotope command line option
-X
ms-index-mzml command line option
ms-index-mzmlb command line option
-z
ms-index-mgf command line option
ms-index-mzml command line option
ms-index-mzmlb command line option
_
__call__() (ms_deisotope.deconvolution.peak_retention_strategy.PeakRetentionStrategyBase method)
(ms_deisotope.scoring.IsotopicFitterBase method)
_Index (class in ms_deisotope.peak_set)
A
a_to_a2_ratio (ms_deisotope.peak_set.DeconvolutedPeak attribute)
acquisition_information (ms_deisotope.data_source.common.Scan attribute)
(ms_deisotope.data_source.common.Scan property)
activation (ms_deisotope.data_source.common.Scan attribute)
(ms_deisotope.data_source.common.Scan property)
ActivationInformation (class in ms_deisotope.data_source.common)
(class in ms_deisotope.data_source.metadata.activation)
add_content() (ms_deisotope.data_source.metadata.file_information.FileInformation method)
add_data_processing() (ms_deisotope.output.mzml.MzMLSerializer method)
(ms_deisotope.output.mzmlb.MzMLbSerializer method)
add_file() (ms_deisotope.data_source.metadata.file_information.FileInformation method)
add_file_contents() (ms_deisotope.output.mzml.MzMLSerializer method)
(ms_deisotope.output.mzmlb.MzMLbSerializer method)
add_file_information() (ms_deisotope.output.mzml.MzMLSerializer method)
(ms_deisotope.output.mzmlb.MzMLbSerializer method)
add_global_parameter() (ms_deisotope.output.mgf.MGFSerializer method)
add_instrument_configuration() (ms_deisotope.output.mzml.MzMLSerializer method)
(ms_deisotope.output.mzmlb.MzMLbSerializer method)
add_parameter() (ms_deisotope.output.mgf.MGFSerializer method)
add_processing_parameter() (ms_deisotope.output.mzml.MzMLSerializer method)
(ms_deisotope.output.mzmlb.MzMLbSerializer method)
add_software() (ms_deisotope.output.mzml.MzMLSerializer method)
,
[1]
(ms_deisotope.output.mzmlb.MzMLbSerializer method)
,
[1]
add_source_file() (ms_deisotope.output.mzml.MzMLSerializer method)
(ms_deisotope.output.mzmlb.MzMLbSerializer method)
all_peaks_for() (ms_deisotope.peak_set.DeconvolutedPeakSet method)
analyzer_types (in module ms_deisotope.data_source.metadata.instrument_components)
annotate_isotopic_peaks() (in module ms_deisotope.plot)
annotate_precursors() (ms_deisotope.data_source.common.ScanBunch method)
annotate_scan() (in module ms_deisotope.plot)
annotate_scan_single() (in module ms_deisotope.plot)
annotations (ms_deisotope.data_source.common.Scan attribute)
(ms_deisotope.data_source.common.Scan property)
arrays (ms_deisotope.data_source.common.Scan attribute)
(ms_deisotope.data_source.common.Scan property)
average() (ms_deisotope.data_source.common.Scan method)
average_mass (ms_deisotope.peak_set.DeconvolutedPeak attribute)
average_with() (ms_deisotope.data_source.common.Scan method)
Averagine (class in ms_deisotope.averagine)
averagine (ms_deisotope.averagine.AveragineCache attribute)
(ms_deisotope.deconvolution.AveragineDeconvoluter attribute)
(ms_deisotope.deconvolution.AveragineDeconvoluterBase attribute)
(ms_deisotope.deconvolution.AveraginePeakDependenceGraphDeconvoluter attribute)
AveragineCache (class in ms_deisotope.averagine)
AveragineDeconvoluter (class in ms_deisotope.deconvolution)
AveragineDeconvoluterBase (class in ms_deisotope.deconvolution)
AveraginePeakDependenceGraphDeconvoluter (class in ms_deisotope.deconvolution)
B
base_composition (ms_deisotope.averagine.Averagine attribute)
base_mass (ms_deisotope.averagine.Averagine attribute)
base_peak_chromatogram_tracker (ms_deisotope.output.mzml.MzMLSerializer attribute)
base_peak_coefficient (ms_deisotope.deconvolution.peak_retention_strategy.TopNRetentionStrategy attribute)
between() (ms_deisotope.deconvolution.DeconvoluterBase method)
(ms_deisotope.peak_set.DeconvolutedPeakSet method)
between_mz() (ms_deisotope.data_source.common.RawDataArrays method)
bind() (ms_deisotope.data_source.common.PrecursorInformation method)
(ms_deisotope.data_source.common.Scan method)
C
cache_truncation (ms_deisotope.averagine.AveragineCache attribute)
category (ms_deisotope.data_source.metadata.cv.Term attribute)
charge (ms_deisotope.data_source.common.PrecursorInformation attribute)
(ms_deisotope.peak_set.DeconvolutedPeak attribute)
(ms_deisotope.processor.PriorityTarget attribute)
(ms_deisotope.scoring.IsotopicFitRecord attribute)
charge_range_hint() (ms_deisotope.processor.PriorityTarget method)
charge_state_determination() (ms_deisotope.deconvolution.AveragineDeconvoluter method)
(ms_deisotope.deconvolution.AveraginePeakDependenceGraphDeconvoluter method)
(ms_deisotope.deconvolution.ExhaustivePeakSearchDeconvoluterBase method)
chromatogram_queue (ms_deisotope.output.mzml.MzMLSerializer attribute)
clear() (ms_deisotope.data_source.common.Scan method)
clone() (ms_deisotope.data_source.common.PrecursorInformation method)
(ms_deisotope.data_source.common.Scan method)
close() (ms_deisotope.data_source.common.ScanDataSource method)
(ms_deisotope.data_source.mgf.MGFLoader method)
(ms_deisotope.data_source.mzml.MzMLLoader method)
(ms_deisotope.data_source.mzmlb.MzMLbLoader method)
(ms_deisotope.data_source.mzxml.MzXMLLoader method)
(ms_deisotope.data_source.thermo_raw_net.ThermoRawLoader method)
(ms_deisotope.output.mzml.MzMLSerializer method)
(ms_deisotope.output.mzmlb.MzMLbSerializer method)
combination (ms_deisotope.data_source.common.ScanAcquisitionInformation attribute)
Component (class in ms_deisotope.data_source.metadata.instrument_components)
ComponentGroup (class in ms_deisotope.data_source.metadata.instrument_components)
composition_list (ms_deisotope.deconvolution.CompositionListDeconvoluter attribute)
(ms_deisotope.deconvolution.CompositionListDeconvoluterBase attribute)
(ms_deisotope.deconvolution.CompositionListPeakDependenceGraphDeconvoluter attribute)
CompositionListDeconvoluter (class in ms_deisotope.deconvolution)
CompositionListDeconvoluterBase (class in ms_deisotope.deconvolution)
CompositionListPeakDependenceGraphDeconvoluter (class in ms_deisotope.deconvolution)
compression (ms_deisotope.output.mzml.MzMLSerializer attribute)
content_keys (in module ms_deisotope.data_source.metadata.file_information)
contents (ms_deisotope.data_source.metadata.file_information.FileInformation attribute)
copy() (ms_deisotope.data_source.common.PrecursorInformation method)
(ms_deisotope.data_source.common.RawDataArrays method)
(ms_deisotope.data_source.common.ScanAcquisitionInformation method)
(ms_deisotope.data_source.metadata.file_information.FileInformation method)
correct_mz() (ms_deisotope.data_source.common.PrecursorInformation method)
create_peak() (ms_deisotope.deconvolution.peak_retention_strategy.PeakRetentionStrategyBase method)
cv_psims (in module ms_deisotope.data_source.metadata.cv)
D
data (ms_deisotope.data_source.common.ActivationInformation attribute)
(ms_deisotope.data_source.metadata.activation.ActivationInformation attribute)
(ms_deisotope.data_source.metadata.activation.MultipleActivationInformation attribute)
(ms_deisotope.scoring.IsotopicFitRecord attribute)
data_encoding (ms_deisotope.output.mzml.MzMLSerializer attribute)
data_processing() (ms_deisotope.data_source.mgf.MGFLoader method)
(ms_deisotope.data_source.mzml.MzMLLoader method)
(ms_deisotope.data_source.mzmlb.MzMLbLoader method)
(ms_deisotope.data_source.mzxml.MzXMLLoader method)
(ms_deisotope.data_source.thermo_raw_net.ThermoRawLoader method)
data_processing_list (ms_deisotope.output.mzml.MzMLSerializer attribute)
data_source (ms_deisotope.processor.ScanProcessor attribute)
decharge() (in module ms_deisotope.peak_set)
decode_binary (ms_deisotope.data_source.mzml.MzMLLoader property)
(ms_deisotope.data_source.mzmlb.MzMLbLoader property)
deconvolute() (ms_deisotope.data_source.common.Scan method)
(ms_deisotope.deconvolution.AveragineDeconvoluter method)
(ms_deisotope.deconvolution.AveraginePeakDependenceGraphDeconvoluter method)
(ms_deisotope.deconvolution.CompositionListDeconvoluter method)
(ms_deisotope.deconvolution.CompositionListPeakDependenceGraphDeconvoluter method)
(ms_deisotope.deconvolution.ExhaustivePeakSearchDeconvoluterBase method)
(ms_deisotope.deconvolution.PeakDependenceGraphDeconvoluterBase method)
deconvolute_composition() (ms_deisotope.deconvolution.CompositionListDeconvoluter method)
(ms_deisotope.deconvolution.CompositionListDeconvoluterBase method)
(ms_deisotope.deconvolution.CompositionListPeakDependenceGraphDeconvoluter method)
deconvolute_peak() (ms_deisotope.deconvolution.ExhaustivePeakSearchDeconvoluterBase method)
deconvolute_peaks() (in module ms_deisotope.deconvolution)
deconvolute_precursor_scan() (ms_deisotope.processor.ScanProcessor method)
deconvolute_product_scan() (ms_deisotope.processor.ScanProcessor method)
deconvoluted (ms_deisotope.output.mzml.MzMLSerializer attribute)
deconvoluted_peak_set (ms_deisotope.data_source.common.Scan attribute)
DeconvolutedPeak (class in ms_deisotope.peak_set)
DeconvolutedPeakSet (class in ms_deisotope.peak_set)
DeconvolutedPeakSolution (class in ms_deisotope.peak_set)
deconvoluter (ms_deisotope.utils.DeconvolutionProcessResult attribute)
(ms_deisotope.utils.TargetedDeconvolutionResultBase attribute)
DeconvoluterBase (class in ms_deisotope.deconvolution)
DeconvolutionProcessResult (class in ms_deisotope.utils)
default() (ms_deisotope.data_source.common.PrecursorInformation method)
default_precursor_ion_selection_window (ms_deisotope.processor.ScanProcessor attribute)
defaulted (ms_deisotope.data_source.common.PrecursorInformation attribute)
denoise() (ms_deisotope.data_source.common.Scan method)
description (ms_deisotope.data_source.metadata.cv.Term attribute)
detector_types (in module ms_deisotope.data_source.metadata.instrument_components)
dissociation_methods (in module ms_deisotope.data_source.metadata.activation)
DissociationMethod (class in ms_deisotope.data_source.metadata.activation)
draw_peaklist() (in module ms_deisotope.plot)
draw_raw() (in module ms_deisotope.plot)
drift_time (ms_deisotope.data_source.common.Scan attribute)
E
empty() (ms_deisotope.data_source.common.RawDataArrays class method)
energies (ms_deisotope.data_source.metadata.activation.MultipleActivationInformation attribute)
energy (ms_deisotope.data_source.common.ActivationInformation attribute)
(ms_deisotope.data_source.metadata.activation.ActivationInformation attribute)
Envelope (class in ms_deisotope.peak_set)
envelope (ms_deisotope.peak_set.DeconvolutedPeak attribute)
envelopes_to_peak_set() (in module ms_deisotope.peak_set)
errors (ms_deisotope.utils.DeconvolutionProcessResult attribute)
evaluate() (ms_deisotope.scoring.IsotopicFitterBase method)
ExhaustivePeakSearchDeconvoluterBase (class in ms_deisotope.deconvolution)
experimental (ms_deisotope.scoring.IsotopicFitRecord attribute)
extended_index (ms_deisotope.output.mzml.ProcessedMzMLLoader attribute)
extract() (ms_deisotope.data_source.common.PrecursorInformation method)
extracted_charge (ms_deisotope.data_source.common.PrecursorInformation attribute)
extracted_intensity (ms_deisotope.data_source.common.PrecursorInformation attribute)
extracted_mz (ms_deisotope.data_source.common.PrecursorInformation property)
extracted_neutral_mass (ms_deisotope.data_source.common.PrecursorInformation attribute)
extracted_peak (ms_deisotope.data_source.common.PrecursorInformation attribute)
F
file_contents_list (ms_deisotope.output.mzml.MzMLSerializer attribute)
file_description() (ms_deisotope.data_source.mgf.MGFLoader method)
(ms_deisotope.data_source.mzml.MzMLLoader method)
(ms_deisotope.data_source.mzmlb.MzMLbLoader method)
(ms_deisotope.data_source.mzxml.MzXMLLoader method)
(ms_deisotope.data_source.thermo_raw_net.ThermoRawLoader method)
file_format (ms_deisotope.data_source.metadata.file_information.SourceFile attribute)
file_formats (in module ms_deisotope.data_source.metadata.file_information)
FileInformation (class in ms_deisotope.data_source.metadata.file_information)
find_monoisotopic_peak() (ms_deisotope.data_source.common.PrecursorInformation method)
find_mz() (ms_deisotope.data_source.common.RawDataArrays method)
find_next_ms1() (ms_deisotope.data_source.common.RandomAccessScanSource method)
(ms_deisotope.data_source.mgf.MGFLoader method)
(ms_deisotope.data_source.mzml.MzMLLoader method)
(ms_deisotope.data_source.mzmlb.MzMLbLoader method)
(ms_deisotope.data_source.mzxml.MzXMLLoader method)
(ms_deisotope.data_source.thermo_raw_net.ThermoRawLoader method)
find_previous_ms1() (ms_deisotope.data_source.common.RandomAccessScanSource method)
(ms_deisotope.data_source.mgf.MGFLoader method)
(ms_deisotope.data_source.mzml.MzMLLoader method)
(ms_deisotope.data_source.mzmlb.MzMLbLoader method)
(ms_deisotope.data_source.mzxml.MzXMLLoader method)
(ms_deisotope.data_source.thermo_raw_net.ThermoRawLoader method)
fit (ms_deisotope.peak_set.DeconvolutedPeakSolution attribute)
fit_composition_at_charge() (ms_deisotope.deconvolution.CompositionListDeconvoluterBase method)
fit_incremental_truncation() (ms_deisotope.deconvolution.DeconvoluterBase method)
fit_theoretical_distribution() (ms_deisotope.deconvolution.AveragineDeconvoluterBase method)
FitSelectorBase (class in ms_deisotope.scoring)
from_path() (ms_deisotope.data_source.metadata.file_information.SourceFile class method)
full_width_at_half_max (ms_deisotope.peak_set.DeconvolutedPeak attribute)
FunctionScorer (class in ms_deisotope.scoring)
G
generate_theoretical_isotopic_cluster() (ms_deisotope.deconvolution.CompositionListDeconvoluterBase method)
get() (ms_deisotope.peak_dependency_network.NetworkedTargetedDeconvolutionResult method)
(ms_deisotope.utils.TargetedDeconvolutionResultBase method)
get_content() (ms_deisotope.data_source.metadata.file_information.FileInformation method)
get_index_information_by_scan_id() (ms_deisotope.output.mzml.ProcessedMzMLLoader method)
(ms_deisotope.output.mzmlb.ProcessedMzMLbLoader method)
get_scan_by_id() (ms_deisotope.data_source.common.RandomAccessScanSource method)
(ms_deisotope.data_source.common.ScanBunch method)
(ms_deisotope.data_source.mgf.MGFLoader method)
(ms_deisotope.data_source.mzml.MzMLLoader method)
(ms_deisotope.data_source.mzmlb.MzMLbLoader method)
(ms_deisotope.data_source.mzxml.MzXMLLoader method)
(ms_deisotope.data_source.thermo_raw_net.ThermoRawLoader method)
get_scan_by_index() (ms_deisotope.data_source.common.RandomAccessScanSource method)
(ms_deisotope.data_source.mgf.MGFLoader method)
(ms_deisotope.data_source.mzml.MzMLLoader method)
(ms_deisotope.data_source.mzmlb.MzMLbLoader method)
(ms_deisotope.data_source.mzxml.MzXMLLoader method)
(ms_deisotope.data_source.thermo_raw_net.ThermoRawLoader method)
get_scan_by_time() (ms_deisotope.data_source.common.RandomAccessScanSource method)
(ms_deisotope.data_source.mgf.MGFLoader method)
(ms_deisotope.data_source.mzml.MzMLLoader method)
(ms_deisotope.data_source.mzmlb.MzMLbLoader method)
(ms_deisotope.data_source.mzxml.MzXMLLoader method)
(ms_deisotope.data_source.thermo_raw_net.ThermoRawLoader method)
grouped
GTestFitter (class in ms_deisotope.scoring)
H
handle (ms_deisotope.output.mzml.MzMLSerializer attribute)
has_array() (ms_deisotope.data_source.common.RawDataArrays method)
has_content() (ms_deisotope.data_source.metadata.file_information.FileInformation method)
has_fast_random_access (ms_deisotope.data_source.common.RandomAccessScanSource property)
(ms_deisotope.data_source.mgf.MGFLoader property)
(ms_deisotope.data_source.mzml.MzMLLoader property)
(ms_deisotope.data_source.mzmlb.MzMLbLoader property)
(ms_deisotope.data_source.mzxml.MzXMLLoader property)
(ms_deisotope.data_source.thermo_raw_net.ThermoRawLoader property)
has_index_file() (ms_deisotope.output.mzml.ProcessedMzMLLoader method)
(ms_deisotope.output.mzmlb.ProcessedMzMLbLoader method)
has_ms1_scans() (ms_deisotope.data_source.common.ScanIterator method)
(ms_deisotope.data_source.mgf.MGFLoader method)
(ms_deisotope.data_source.mzml.MzMLLoader method)
(ms_deisotope.data_source.mzmlb.MzMLbLoader method)
(ms_deisotope.data_source.mzxml.MzXMLLoader method)
(ms_deisotope.data_source.thermo_raw_net.ThermoRawLoader method)
has_msn_scans() (ms_deisotope.data_source.common.ScanIterator method)
(ms_deisotope.data_source.mgf.MGFLoader method)
(ms_deisotope.data_source.mzml.MzMLLoader method)
(ms_deisotope.data_source.mzmlb.MzMLbLoader method)
(ms_deisotope.data_source.mzxml.MzXMLLoader method)
(ms_deisotope.data_source.thermo_raw_net.ThermoRawLoader method)
has_peak() (ms_deisotope.data_source.common.Scan method)
(ms_deisotope.deconvolution.DeconvoluterBase method)
(ms_deisotope.peak_set.DeconvolutedPeakSet method)
has_supplemental_dissociation() (ms_deisotope.data_source.common.ActivationInformation method)
(ms_deisotope.data_source.metadata.activation.ActivationInformation method)
(ms_deisotope.data_source.metadata.activation.MultipleActivationInformation method)
header (ms_deisotope.data_source.mgf.MGFLoader attribute)
(ms_deisotope.data_source.mgf.MGFLoader property)
I
id (ms_deisotope.data_source.common.Scan attribute)
(ms_deisotope.data_source.common.Scan property)
(ms_deisotope.data_source.metadata.cv.Term attribute)
(ms_deisotope.data_source.metadata.file_information.SourceFile attribute)
id_format (ms_deisotope.data_source.metadata.file_information.SourceFile attribute)
id_formats (in module ms_deisotope.data_source.metadata.file_information)
ignore_below() (ms_deisotope.averagine.TheoreticalIsotopicPattern method)
incremental_truncation (ms_deisotope.deconvolution.ExhaustivePeakSearchDeconvoluterBase attribute)
index (ms_deisotope.data_source.common.Scan attribute)
(ms_deisotope.data_source.common.Scan property)
(ms_deisotope.data_source.mgf.MGFLoader property)
(ms_deisotope.data_source.mzml.MzMLLoader property)
(ms_deisotope.data_source.mzmlb.MzMLbLoader property)
(ms_deisotope.data_source.mzxml.MzXMLLoader property)
(ms_deisotope.data_source.thermo_raw_net.ThermoRawLoader property)
(ms_deisotope.peak_set.DeconvolutedPeak attribute)
indexer (ms_deisotope.output.mzml.MzMLSerializer attribute)
infer_minimum_charge() (ms_deisotope.deconvolution.peak_retention_strategy.PeakRetentionStrategyBase method)
info (ms_deisotope.processor.PriorityTarget attribute)
initialize_scan_cache() (ms_deisotope.data_source.common.ScanIterator method)
(ms_deisotope.data_source.mgf.MGFLoader method)
(ms_deisotope.data_source.mzml.MzMLLoader method)
(ms_deisotope.data_source.mzmlb.MzMLbLoader method)
(ms_deisotope.data_source.mzxml.MzXMLLoader method)
(ms_deisotope.data_source.thermo_raw_net.ThermoRawLoader method)
inlet_types (in module ms_deisotope.data_source.metadata.instrument_components)
insert() (ms_deisotope.data_source.common.ScanAcquisitionInformation method)
instrument_configuration (ms_deisotope.data_source.common.Scan attribute)
(ms_deisotope.data_source.common.Scan property)
instrument_configuration() (ms_deisotope.data_source.mgf.MGFLoader method)
(ms_deisotope.data_source.mzml.MzMLLoader method)
(ms_deisotope.data_source.mzmlb.MzMLbLoader method)
(ms_deisotope.data_source.mzxml.MzXMLLoader method)
(ms_deisotope.data_source.thermo_raw_net.ThermoRawLoader method)
instrument_configuration_list (ms_deisotope.output.mzml.MzMLSerializer attribute)
InstrumentInformation (class in ms_deisotope.data_source.metadata.instrument_components)
intensity (ms_deisotope.data_source.common.PrecursorInformation attribute)
(ms_deisotope.data_source.common.RawDataArrays attribute)
(ms_deisotope.peak_set.DeconvolutedPeak attribute)
ionization_types (in module ms_deisotope.data_source.metadata.instrument_components)
is_a() (ms_deisotope.data_source.metadata.cv.Term method)
(ms_deisotope.data_source.metadata.instrument_components.Component method)
is_empty() (ms_deisotope.data_source.common.IsolationWindow method)
is_maximizing() (ms_deisotope.scoring.IsotopicFitterBase method)
is_multiple_dissociation() (ms_deisotope.data_source.common.ActivationInformation method)
(ms_deisotope.data_source.metadata.activation.ActivationInformation method)
(ms_deisotope.data_source.metadata.activation.MultipleActivationInformation method)
is_profile (ms_deisotope.data_source.common.Scan attribute)
(ms_deisotope.data_source.common.Scan property)
is_supplemental() (ms_deisotope.data_source.metadata.activation.DissociationMethod method)
isolation_window (ms_deisotope.data_source.common.Scan attribute)
(ms_deisotope.data_source.common.Scan property)
(ms_deisotope.processor.PriorityTarget attribute)
IsolationWindow (class in ms_deisotope.data_source.common)
isotopic_cluster() (ms_deisotope.averagine.Averagine method)
(ms_deisotope.averagine.AveragineCache method)
IsotopicFitRecord (class in ms_deisotope.scoring)
IsotopicFitterBase (class in ms_deisotope.scoring)
iteration_mode (ms_deisotope.data_source.common.ScanIterator attribute)
L
label_peaks() (in module ms_deisotope.plot)
LeastSquaresFitter (class in ms_deisotope.scoring)
loader_type (ms_deisotope.processor.ScanProcessor attribute)
location (ms_deisotope.data_source.metadata.file_information.SourceFile attribute)
lower (ms_deisotope.data_source.common.IsolationWindow attribute)
lower_bound (ms_deisotope.data_source.common.IsolationWindow attribute)
(ms_deisotope.data_source.common.IsolationWindow property)
M
make_empty() (ms_deisotope.data_source.common.IsolationWindow class method)
make_iterator() (ms_deisotope.data_source.common.ScanIterator method)
(ms_deisotope.data_source.mgf.MGFLoader method)
(ms_deisotope.data_source.mzml.MzMLLoader method)
(ms_deisotope.data_source.mzmlb.MzMLbLoader method)
(ms_deisotope.data_source.mzxml.MzXMLLoader method)
(ms_deisotope.data_source.thermo_raw_net.ThermoRawLoader method)
match_theoretical_isotopic_distribution() (ms_deisotope.deconvolution.DeconvoluterBase method)
max_mass (ms_deisotope.deconvolution.peak_retention_strategy.TopNRetentionStrategy attribute)
max_missed_peaks (ms_deisotope.deconvolution.AveraginePeakDependenceGraphDeconvoluter attribute)
(ms_deisotope.deconvolution.CompositionListPeakDependenceGraphDeconvoluter attribute)
(ms_deisotope.deconvolution.PeakDependenceGraphDeconvoluterBase attribute)
(ms_deisotope.deconvolution.PeakDependenceGraphDeconvoluterBase property)
MaximizeFitSelector (class in ms_deisotope.scoring)
members (ms_deisotope.data_source.metadata.instrument_components.ComponentGroup attribute)
merge() (in module ms_deisotope.peak_set)
merge_isobaric_peaks (ms_deisotope.deconvolution.AveraginePeakDependenceGraphDeconvoluter attribute)
(ms_deisotope.deconvolution.CompositionListDeconvoluter attribute)
(ms_deisotope.deconvolution.CompositionListPeakDependenceGraphDeconvoluter attribute)
(ms_deisotope.deconvolution.DeconvoluterBase attribute)
,
[1]
method (ms_deisotope.data_source.common.ActivationInformation attribute)
(ms_deisotope.data_source.metadata.activation.ActivationInformation attribute)
methods (ms_deisotope.data_source.metadata.activation.MultipleActivationInformation attribute)
mgf
MGF
mgf
M
MGFLoader (class in ms_deisotope.data_source.mgf)
MGFSerializer (class in ms_deisotope.output.mgf)
MinimizeFitSelector (class in ms_deisotope.scoring)
minimum_intensity (ms_deisotope.deconvolution.AveraginePeakDependenceGraphDeconvoluter attribute)
(ms_deisotope.deconvolution.CompositionListDeconvoluter attribute)
(ms_deisotope.deconvolution.CompositionListPeakDependenceGraphDeconvoluter attribute)
(ms_deisotope.deconvolution.DeconvoluterBase attribute)
,
[1]
minimum_score (ms_deisotope.scoring.FitSelectorBase attribute)
missed_peaks (ms_deisotope.scoring.IsotopicFitRecord attribute)
module
ms_deisotope.averagine
ms_deisotope.data_source.common
,
[1]
ms_deisotope.data_source.metadata.activation
ms_deisotope.data_source.metadata.cv
ms_deisotope.data_source.metadata.file_information
ms_deisotope.data_source.metadata.instrument_components
ms_deisotope.data_source.mgf
ms_deisotope.data_source.mzml
ms_deisotope.data_source.mzmlb
ms_deisotope.data_source.mzxml
ms_deisotope.data_source.thermo_raw_net
ms_deisotope.deconvolution
ms_deisotope.deconvolution.peak_retention_strategy
ms_deisotope.deconvolution.utils
ms_deisotope.output.mgf
ms_deisotope.output.mzml
ms_deisotope.output.mzmlb
ms_deisotope.peak_dependency_network
ms_deisotope.peak_set
ms_deisotope.plot
ms_deisotope.processor
ms_deisotope.scoring
ms_deisotope.utils
monoisotopic_peak (ms_deisotope.scoring.IsotopicFitRecord attribute)
most_abundant_mass (ms_deisotope.peak_set.DeconvolutedPeak attribute)
ms-deisotope command line option
--averagine <averagine>
--background-reduction <float>
--default-precursor-ion-selection-window <float>
--end-time <float>
--extract-only-tandem-envelopes
--ignore-msn
--isotopic-strictness <float>
--mass-offset <float>
--maximum-charge <int>
--missed-peaks <int>
--ms1-averaging <int>
--msn-averagine <averagine>
--msn-background-reduction <float>
--msn-isotopic-strictness <float>
--msn-missed-peaks <int>
--msn-score-threshold <float>
--msn-transform <func>
--name <string>
--processes <int>
--score-threshold <float>
--signal-to-noise-threshold <float>
--start-time <float>
--transform <func>
--verbose
-a
-an
-b
-bn
-c
-D
-e
-g
-i
-in
-m
-mn
-mo
-n
-p
-r
-rn
-s
-snr
-t
-tn
-v
MS_FILE
OUTFILE_PATH
ms-index-byte-index command line option
PATHS
ms-index-charge-states command line option
PATH
ms-index-describe command line option
--diagnostics
-d
PATH
ms-index-metadata-index command line option
--deconvoluted
--processes <int>
-D
-p
PATHS
ms-index-mgf command line option
--compress
--msn-filter <func>
-rn
-z
OUTPUT
SOURCE
ms-index-msms-intervals command line option
--output <path>
--processes <int>
-o
-p
PATHS
ms-index-mzml command line option
--compress
--correct-precursor-mz
--ms1-filter <func>
--msn-filter <func>
--no-update-metadata
--option <tuple>
--pick-peaks
--reprofile
--update-metadata
-c
-f
-p
-r
-rn
-X
-z
OUTPUT
SOURCE
ms-index-mzmlb command line option
--compression <choice>
--correct-precursor-mz
--ms1-filter <func>
--msn-filter <func>
--no-update-metadata
--option <tuple>
--pick-peaks
--reprofile
--update-metadata
-c
-f
-p
-r
-rn
-X
-z
OUTPUT
SOURCE
ms-index-precursor-clustering command line option
PATH
ms-index-spectrum-clustering command line option
--cache-size <int>
--deconvoluted
--in-memory
--output <path>
--precursor-error-tolerance <float>
--similarity-threshold <float>
-c
-D
-m
-M
-o
-t
PATHS
ms1_averaging (ms_deisotope.processor.ScanProcessor attribute)
ms1_deconvolution_args (ms_deisotope.processor.ScanProcessor attribute)
ms1_peak_picking_args (ms_deisotope.processor.ScanProcessor attribute)
ms_deisotope.averagine
module
ms_deisotope.data_source.common
module
,
[1]
ms_deisotope.data_source.metadata.activation
module
ms_deisotope.data_source.metadata.cv
module
ms_deisotope.data_source.metadata.file_information
module
ms_deisotope.data_source.metadata.instrument_components
module
ms_deisotope.data_source.mgf
module
ms_deisotope.data_source.mzml
module
ms_deisotope.data_source.mzmlb
module
ms_deisotope.data_source.mzxml
module
ms_deisotope.data_source.thermo_raw_net
module
ms_deisotope.deconvolution
module
ms_deisotope.deconvolution.peak_retention_strategy
module
ms_deisotope.deconvolution.utils
module
ms_deisotope.output.mgf
module
ms_deisotope.output.mzml
module
ms_deisotope.output.mzmlb
module
ms_deisotope.peak_dependency_network
module
ms_deisotope.peak_set
module
ms_deisotope.plot
module
ms_deisotope.processor
module
ms_deisotope.scoring
module
ms_deisotope.utils
module
MS_FILE
ms-deisotope command line option
ms_level (ms_deisotope.data_source.common.Scan attribute)
(ms_deisotope.data_source.common.Scan property)
MSDeconVFitter (class in ms_deisotope.scoring)
msn_deconvolution_args (ms_deisotope.processor.ScanProcessor attribute)
msn_peak_picking_args (ms_deisotope.processor.ScanProcessor attribute)
MultipleActivationInformation (class in ms_deisotope.data_source.metadata.activation)
mz (ms_deisotope.data_source.common.PrecursorInformation attribute)
(ms_deisotope.data_source.common.RawDataArrays attribute)
(ms_deisotope.peak_set._Index attribute)
(ms_deisotope.peak_set.DeconvolutedPeak attribute)
(ms_deisotope.processor.PriorityTarget attribute)
mzml
mzML
mzml
M
MzMLbLoader (class in ms_deisotope.data_source.mzmlb)
MzMLbSerializer (class in ms_deisotope.output.mzmlb)
MzMLLoader (class in ms_deisotope.data_source.mzml)
MzMLSerializer (class in ms_deisotope.output.mzml)
MzXMLLoader (class in ms_deisotope.data_source.mzxml)
N
n_peaks (ms_deisotope.deconvolution.peak_retention_strategy.TopNRetentionStrategy attribute)
n_spectra (ms_deisotope.output.mzml.MzMLSerializer attribute)
name (ms_deisotope.data_source.metadata.cv.Term attribute)
(ms_deisotope.data_source.metadata.file_information.SourceFile attribute)
nativeID
nativeID
N
NetworkedTargetedDeconvolutionResult (class in ms_deisotope.peak_dependency_network)
neutral_mass (ms_deisotope.data_source.common.PrecursorInformation property)
(ms_deisotope.peak_set._Index attribute)
(ms_deisotope.peak_set.DeconvolutedPeak attribute)
next() (ms_deisotope.data_source.common.ScanIterator method)
(ms_deisotope.data_source.mgf.MGFLoader method)
(ms_deisotope.data_source.mzml.MzMLLoader method)
(ms_deisotope.data_source.mzmlb.MzMLbLoader method)
(ms_deisotope.data_source.mzxml.MzXMLLoader method)
(ms_deisotope.data_source.thermo_raw_net.ThermoRawLoader method)
(ms_deisotope.processor.ScanProcessor method)
O
order (ms_deisotope.data_source.metadata.instrument_components.ComponentGroup attribute)
origin (ms_deisotope.averagine.TheoreticalIsotopicPattern attribute)
orphan (ms_deisotope.data_source.common.PrecursorInformation attribute)
OUTFILE_PATH
ms-deisotope command line option
OUTPUT
ms-index-mgf command line option
ms-index-mzml command line option
ms-index-mzmlb command line option
P
pack() (ms_deisotope.data_source.common.Scan method)
(ms_deisotope.data_source.common.ScanBunch method)
pairs (ms_deisotope.peak_set.Envelope attribute)
parameters (ms_deisotope.data_source.metadata.file_information.SourceFile attribute)
PATH
ms-index-charge-states command line option
ms-index-describe command line option
ms-index-precursor-clustering command line option
PATHS
ms-index-byte-index command line option
ms-index-metadata-index command line option
ms-index-msms-intervals command line option
ms-index-spectrum-clustering command line option
peak (ms_deisotope.data_source.common.PrecursorInformation attribute)
(ms_deisotope.processor.PriorityTarget attribute)
peak list format
peak_dependency_network (ms_deisotope.deconvolution.AveraginePeakDependenceGraphDeconvoluter attribute)
(ms_deisotope.deconvolution.CompositionListPeakDependenceGraphDeconvoluter attribute)
(ms_deisotope.deconvolution.PeakDependenceGraphDeconvoluterBase attribute)
peak_set (ms_deisotope.data_source.common.Scan attribute)
(ms_deisotope.utils.DeconvolutionProcessResult attribute)
PeakDependenceGraph (class in ms_deisotope.peak_dependency_network)
PeakDependenceGraphDeconvoluterBase (class in ms_deisotope.deconvolution)
peaklist (ms_deisotope.averagine.TheoreticalIsotopicPattern attribute)
(ms_deisotope.deconvolution.AveragineDeconvoluter attribute)
(ms_deisotope.deconvolution.AveraginePeakDependenceGraphDeconvoluter attribute)
(ms_deisotope.deconvolution.CompositionListDeconvoluter attribute)
(ms_deisotope.deconvolution.CompositionListPeakDependenceGraphDeconvoluter attribute)
(ms_deisotope.deconvolution.DeconvoluterBase attribute)
,
[1]
PeakRetentionStrategyBase (class in ms_deisotope.deconvolution.peak_retention_strategy)
PenalizedMSDeconVFitter (class in ms_deisotope.scoring)
pick_only_tandem_envelopes (ms_deisotope.processor.ScanProcessor attribute)
pick_peaks() (ms_deisotope.data_source.common.Scan method)
pick_precursor_scan_peaks() (ms_deisotope.processor.ScanProcessor method)
pick_product_scan_peaks() (ms_deisotope.processor.ScanProcessor method)
plot() (ms_deisotope.data_source.common.RawDataArrays method)
polarity (ms_deisotope.data_source.common.Scan attribute)
(ms_deisotope.data_source.common.Scan property)
populate_graph() (ms_deisotope.deconvolution.AveraginePeakDependenceGraphDeconvoluter method)
(ms_deisotope.deconvolution.CompositionListPeakDependenceGraphDeconvoluter method)
(ms_deisotope.deconvolution.PeakDependenceGraphDeconvoluterBase method)
postprocess_fits() (ms_deisotope.deconvolution.PeakDependenceGraphDeconvoluterBase method)
prebuild_byte_offset_file() (ms_deisotope.data_source.mzml.MzMLLoader class method)
(ms_deisotope.data_source.mzmlb.MzMLbLoader class method)
(ms_deisotope.data_source.mzxml.MzXMLLoader class method)
precursor (ms_deisotope.data_source.common.PrecursorInformation property)
(ms_deisotope.data_source.common.ScanBunch attribute)
precursor_for() (ms_deisotope.data_source.common.ScanBunch method)
precursor_information (ms_deisotope.data_source.common.Scan attribute)
(ms_deisotope.data_source.common.Scan property)
precursor_scan_id (ms_deisotope.data_source.common.PrecursorInformation attribute)
PrecursorInformation (class in ms_deisotope.data_source.common)
prepare_peaklist() (in module ms_deisotope.deconvolution.utils)
priorities (ms_deisotope.utils.DeconvolutionProcessResult attribute)
PriorityTarget (class in ms_deisotope.processor)
process() (in module ms_deisotope.processor)
(ms_deisotope.processor.ScanProcessor method)
process_scan_group() (ms_deisotope.processor.ScanProcessor method)
ProcessedMGFDeserializer (in module ms_deisotope.output.mgf)
ProcessedMzMLbLoader (class in ms_deisotope.output.mzmlb)
ProcessedMzMLLoader (class in ms_deisotope.output.mzml)
processing_parameters (ms_deisotope.output.mzml.MzMLSerializer attribute)
product (ms_deisotope.data_source.common.PrecursorInformation property)
product_scans (ms_deisotope.data_source.common.Scan attribute)
products (ms_deisotope.data_source.common.ScanBunch attribute)
Q
query_peak (ms_deisotope.peak_dependency_network.NetworkedTargetedDeconvolutionResult attribute)
R
RandomAccessScanSource (class in ms_deisotope.data_source.common)
RawDataArrays (class in ms_deisotope.data_source.common)
reader (ms_deisotope.processor.ScanProcessor attribute)
recalibrate_theoretical_mz() (ms_deisotope.deconvolution.CompositionListDeconvoluterBase method)
reject() (ms_deisotope.scoring.IsotopicFitterBase method)
remove_content() (ms_deisotope.data_source.metadata.file_information.FileInformation method)
reprofile() (ms_deisotope.data_source.common.Scan method)
reset() (ms_deisotope.data_source.common.ScanIterator method)
(ms_deisotope.data_source.mgf.MGFLoader method)
(ms_deisotope.data_source.mzml.MzMLLoader method)
(ms_deisotope.data_source.mzmlb.MzMLbLoader method)
(ms_deisotope.data_source.mzxml.MzXMLLoader method)
(ms_deisotope.data_source.thermo_raw_net.ThermoRawLoader method)
respect_isolation_window (ms_deisotope.processor.ScanProcessor attribute)
retain_peaks() (ms_deisotope.deconvolution.peak_retention_strategy.PeakRetentionStrategyBase method)
(ms_deisotope.deconvolution.peak_retention_strategy.TopNRetentionStrategy method)
S
sample_list (ms_deisotope.output.mzml.MzMLSerializer attribute)
sample_name (ms_deisotope.output.mgf.MGFSerializer attribute)
(ms_deisotope.output.mzml.MzMLSerializer attribute)
sample_run (ms_deisotope.output.mzml.MzMLSerializer attribute)
(ms_deisotope.output.mzml.ProcessedMzMLLoader attribute)
samples() (ms_deisotope.data_source.mzml.MzMLLoader method)
(ms_deisotope.data_source.mzmlb.MzMLbLoader method)
(ms_deisotope.data_source.thermo_raw_net.ThermoRawLoader method)
save() (ms_deisotope.output.mzml.MzMLSerializer method)
(ms_deisotope.output.mzmlb.MzMLbSerializer method)
save_scan() (ms_deisotope.output.mzml.MzMLSerializer method)
(ms_deisotope.output.mzmlb.MzMLbSerializer method)
save_scan_bunch() (ms_deisotope.output.mgf.MGFSerializer method)
(ms_deisotope.output.mzml.MzMLSerializer method)
(ms_deisotope.output.mzmlb.MzMLbSerializer method)
scale() (ms_deisotope.averagine.Averagine method)
(ms_deisotope.averagine.TheoreticalIsotopicPattern method)
scale_method (ms_deisotope.deconvolution.AveraginePeakDependenceGraphDeconvoluter attribute)
(ms_deisotope.deconvolution.CompositionListDeconvoluter attribute)
(ms_deisotope.deconvolution.CompositionListPeakDependenceGraphDeconvoluter attribute)
(ms_deisotope.deconvolution.DeconvoluterBase attribute)
,
[1]
scale_theoretical_distribution() (ms_deisotope.deconvolution.DeconvoluterBase method)
ScaledGTestFitter (class in ms_deisotope.scoring)
Scan (class in ms_deisotope.data_source.common)
scan_cache (ms_deisotope.data_source.common.ScanIterator property)
(ms_deisotope.data_source.mgf.MGFLoader property)
(ms_deisotope.data_source.mzml.MzMLLoader property)
(ms_deisotope.data_source.mzmlb.MzMLbLoader property)
(ms_deisotope.data_source.mzxml.MzXMLLoader property)
(ms_deisotope.data_source.thermo_raw_net.ThermoRawLoader property)
scan_id
scan ID
scan id
scan_id
(ms_deisotope.data_source.common.Scan property)
scan_index
scan index
scan number
S
scan_list (ms_deisotope.data_source.common.ScanAcquisitionInformation attribute)
scan_time (ms_deisotope.data_source.common.Scan attribute)
(ms_deisotope.data_source.common.Scan property)
ScanAcquisitionInformation (class in ms_deisotope.data_source.common)
ScanBunch (class in ms_deisotope.data_source.common)
ScanDataSource (class in ms_deisotope.data_source.common)
ScanIterator (class in ms_deisotope.data_source.common)
ScanProcessor (class in ms_deisotope.processor)
score (ms_deisotope.peak_set.DeconvolutedPeak attribute)
(ms_deisotope.scoring.IsotopicFitRecord attribute)
scorer (ms_deisotope.deconvolution.AveragineDeconvoluter attribute)
(ms_deisotope.deconvolution.AveraginePeakDependenceGraphDeconvoluter attribute)
(ms_deisotope.deconvolution.CompositionListDeconvoluter attribute)
(ms_deisotope.deconvolution.CompositionListPeakDependenceGraphDeconvoluter attribute)
(ms_deisotope.deconvolution.DeconvoluterBase attribute)
,
[1]
seed_peak (ms_deisotope.scoring.IsotopicFitRecord attribute)
select_best_disjoint_subgraphs() (ms_deisotope.deconvolution.PeakDependenceGraphDeconvoluterBase method)
shift() (ms_deisotope.averagine.TheoreticalIsotopicPattern method)
signal_to_noise (ms_deisotope.peak_set.DeconvolutedPeak attribute)
single
software_list (ms_deisotope.output.mzml.MzMLSerializer attribute)
software_list() (ms_deisotope.data_source.mgf.MGFLoader method)
(ms_deisotope.data_source.mzml.MzMLLoader method)
(ms_deisotope.data_source.mzmlb.MzMLbLoader method)
(ms_deisotope.data_source.mzxml.MzXMLLoader method)
(ms_deisotope.data_source.thermo_raw_net.ThermoRawLoader method)
solution (ms_deisotope.peak_set.DeconvolutedPeakSolution attribute)
solution_peak (ms_deisotope.peak_dependency_network.NetworkedTargetedDeconvolutionResult attribute)
SOURCE
ms-index-mgf command line option
ms-index-mzml command line option
ms-index-mzmlb command line option
source (ms_deisotope.data_source.common.PrecursorInformation attribute)
(ms_deisotope.data_source.common.Scan attribute)
(ms_deisotope.data_source.mgf.MGFLoader attribute)
(ms_deisotope.data_source.mgf.MGFLoader property)
(ms_deisotope.data_source.mzml.MzMLLoader attribute)
(ms_deisotope.data_source.mzml.MzMLLoader property)
(ms_deisotope.data_source.mzmlb.MzMLbLoader attribute)
(ms_deisotope.data_source.mzmlb.MzMLbLoader property)
(ms_deisotope.data_source.mzxml.MzXMLLoader attribute)
(ms_deisotope.data_source.mzxml.MzXMLLoader property)
source_file (ms_deisotope.data_source.mgf.MGFLoader attribute)
(ms_deisotope.data_source.mzml.MzMLLoader attribute)
(ms_deisotope.data_source.mzmlb.MzMLbLoader attribute)
(ms_deisotope.data_source.mzxml.MzXMLLoader attribute)
source_file_list (ms_deisotope.output.mzml.MzMLSerializer attribute)
source_file_name (ms_deisotope.data_source.common.ScanDataSource property)
(ms_deisotope.data_source.mgf.MGFLoader property)
(ms_deisotope.data_source.mzml.MzMLLoader property)
(ms_deisotope.data_source.mzmlb.MzMLbLoader property)
(ms_deisotope.data_source.mzxml.MzXMLLoader property)
(ms_deisotope.data_source.thermo_raw_net.ThermoRawLoader property)
source_files (ms_deisotope.data_source.metadata.file_information.FileInformation attribute)
SourceFile (class in ms_deisotope.data_source.metadata.file_information)
spans() (ms_deisotope.data_source.common.IsolationWindow method)
specialization (ms_deisotope.data_source.metadata.cv.Term attribute)
start_from_scan() (ms_deisotope.data_source.common.RandomAccessScanSource method)
(ms_deisotope.data_source.mgf.MGFLoader method)
(ms_deisotope.data_source.mzml.MzMLLoader method)
(ms_deisotope.data_source.mzmlb.MzMLbLoader method)
(ms_deisotope.data_source.mzxml.MzXMLLoader method)
(ms_deisotope.data_source.thermo_raw_net.ThermoRawLoader method)
(ms_deisotope.processor.ScanProcessor method)
started (ms_deisotope.output.mgf.MGFSerializer attribute)
subtraction() (ms_deisotope.deconvolution.DeconvoluterBase method)
T
target (ms_deisotope.data_source.common.IsolationWindow attribute)
targeted_deconvolution() (ms_deisotope.deconvolution.AveragineDeconvoluter method)
(ms_deisotope.deconvolution.AveraginePeakDependenceGraphDeconvoluter method)
(ms_deisotope.deconvolution.ExhaustivePeakSearchDeconvoluterBase method)
(ms_deisotope.deconvolution.PeakDependenceGraphDeconvoluterBase method)
TargetedDeconvolutionResultBase (class in ms_deisotope.utils)
Term (class in ms_deisotope.data_source.metadata.cv)
terminate_on_error (ms_deisotope.processor.ScanProcessor attribute)
theoretical (ms_deisotope.scoring.IsotopicFitRecord attribute)
TheoreticalIsotopicPattern (class in ms_deisotope.averagine)
ThermoRawLoader (class in ms_deisotope.data_source.thermo_raw_net)
time (ms_deisotope.data_source.common.RandomAccessScanSource property)
(ms_deisotope.data_source.mgf.MGFLoader property)
(ms_deisotope.data_source.mzml.MzMLLoader property)
(ms_deisotope.data_source.mzmlb.MzMLbLoader property)
(ms_deisotope.data_source.mzxml.MzXMLLoader property)
(ms_deisotope.data_source.thermo_raw_net.ThermoRawLoader property)
title (ms_deisotope.data_source.common.Scan attribute)
(ms_deisotope.data_source.common.Scan property)
TopNRetentionStrategy (class in ms_deisotope.deconvolution.peak_retention_strategy)
total_ion_chromatogram_tracker (ms_deisotope.output.mzml.MzMLSerializer attribute)
transform() (ms_deisotope.data_source.common.Scan method)
truncate_after() (ms_deisotope.averagine.TheoreticalIsotopicPattern method)
trust_charge_hint (ms_deisotope.processor.PriorityTarget attribute)
(ms_deisotope.processor.ScanProcessor attribute)
type (ms_deisotope.data_source.metadata.instrument_components.ComponentGroup attribute)
U
unbind() (ms_deisotope.data_source.common.PrecursorInformation method)
(ms_deisotope.data_source.common.Scan method)
update_to_extracted() (ms_deisotope.data_source.common.PrecursorInformation method)
upper (ms_deisotope.data_source.common.IsolationWindow attribute)
upper_bound (ms_deisotope.data_source.common.IsolationWindow attribute)
(ms_deisotope.data_source.common.IsolationWindow property)
use_quick_charge (ms_deisotope.deconvolution.ExhaustivePeakSearchDeconvoluterBase attribute)
use_subtraction (ms_deisotope.deconvolution.AveraginePeakDependenceGraphDeconvoluter attribute)
(ms_deisotope.deconvolution.CompositionListDeconvoluter attribute)
(ms_deisotope.deconvolution.CompositionListPeakDependenceGraphDeconvoluter attribute)
(ms_deisotope.deconvolution.DeconvoluterBase attribute)
,
[1]
V
verbose (ms_deisotope.deconvolution.AveragineDeconvoluter attribute)
(ms_deisotope.deconvolution.AveraginePeakDependenceGraphDeconvoluter attribute)
(ms_deisotope.deconvolution.CompositionListDeconvoluter attribute)
(ms_deisotope.deconvolution.CompositionListPeakDependenceGraphDeconvoluter attribute)
(ms_deisotope.deconvolution.DeconvoluterBase attribute)
,
[1]
W
width (ms_deisotope.data_source.common.IsolationWindow attribute)
(ms_deisotope.data_source.common.IsolationWindow property)
window_peak_set() (in module ms_deisotope.peak_set)
writer (ms_deisotope.output.mzml.MzMLSerializer attribute)
Contents
