Index

Symbols

--add-ion-mobility ms2pip-correlate command line option ms2pip-predict-batch command line option ms2pip-predict-library command line option --add-retention-time ms2pip-correlate command line option ms2pip-predict-batch command line option ms2pip-predict-library command line option --batch-size ms2pip-predict-library command line option --compute-correlations ms2pip-correlate command line option --config ms2pip-predict-library command line option --logging-level ms2pip command line option --model ms2pip-annotate-spectra command line option ms2pip-correlate command line option ms2pip-get-training-data command line option ms2pip-predict-batch command line option ms2pip-predict-library command line option ms2pip-predict-single command line option --model-dir ms2pip-correlate command line option ms2pip-predict-batch command line option ms2pip-predict-library command line option ms2pip-predict-single command line option --ms2-tolerance ms2pip-annotate-spectra command line option ms2pip-correlate command line option ms2pip-get-training-data command line option --output-format ms2pip-predict-batch command line option ms2pip-predict-library command line option ms2pip-predict-single command line option --output-name ms2pip-annotate-spectra command line option ms2pip-correlate command line option ms2pip-get-training-data command line option ms2pip-predict-batch command line option ms2pip-predict-library command line option ms2pip-predict-single command line option --plot ms2pip-predict-single command line option --processes ms2pip-annotate-spectra command line option ms2pip-correlate command line option ms2pip-get-training-data command line option ms2pip-predict-batch command line option ms2pip-predict-library command line option

--psm-filetype ms2pip-annotate-spectra command line option ms2pip-correlate command line option ms2pip-get-training-data command line option ms2pip-predict-batch command line option --spectrum-id-pattern ms2pip-annotate-spectra command line option ms2pip-correlate command line option ms2pip-get-training-data command line option --version ms2pip command line option -c ms2pip-predict-library command line option -f ms2pip-predict-batch command line option ms2pip-predict-library command line option ms2pip-predict-single command line option -i ms2pip-correlate command line option ms2pip-predict-batch command line option ms2pip-predict-library command line option -l ms2pip command line option -n ms2pip-annotate-spectra command line option ms2pip-correlate command line option ms2pip-get-training-data command line option ms2pip-predict-batch command line option ms2pip-predict-library command line option -o ms2pip-annotate-spectra command line option ms2pip-correlate command line option ms2pip-get-training-data command line option ms2pip-predict-batch command line option ms2pip-predict-library command line option ms2pip-predict-single command line option -p ms2pip-annotate-spectra command line option ms2pip-correlate command line option ms2pip-get-training-data command line option ms2pip-predict-single command line option -r ms2pip-correlate command line option ms2pip-predict-batch command line option ms2pip-predict-library command line option -t ms2pip-annotate-spectra command line option ms2pip-correlate command line option ms2pip-get-training-data command line option ms2pip-predict-batch command line option -x ms2pip-correlate command line option

A

annotate_spectra() (in module ms2pip)

as_spectra() (ms2pip.result.ProcessingResult method)

B

Bibliospec (class in ms2pip.spectrum_output)

build() (ms2pip.search_space.ProteomeSearchSpace method)

C

calculate_correlations() (in module ms2pip.result) clip_intensity() (ms2pip.spectrum.Spectrum method)

close() (ms2pip.spectrum_output.Bibliospec method) correlate() (in module ms2pip)

D

DLIB (class in ms2pip.spectrum_output)

download_models() (in module ms2pip)

F

FASTA_FILE ms2pip-predict-library command line option

filter_psms_by_mz() (ms2pip.search_space.ProteomeSearchSpace method) from_any() (ms2pip.search_space.ProteomeSearchSpace class method)

G

get_training_data() (in module ms2pip)

I

InvalidAminoAcidError InvalidInputError

InvalidPeptidoformError InvalidXGBoostModelError

L

log2_transform() (ms2pip.spectrum.Spectrum method)

M

MGF (class in ms2pip.spectrum_output) model_computed_fields (ms2pip.result.ProcessingResult attribute) (ms2pip.search_space.ModificationConfig attribute) (ms2pip.search_space.ProteomeSearchSpace attribute) (ms2pip.spectrum.ObservedSpectrum attribute) (ms2pip.spectrum.PredictedSpectrum attribute) (ms2pip.spectrum.Spectrum attribute) model_config (ms2pip.result.ProcessingResult attribute) (ms2pip.search_space.ModificationConfig attribute) (ms2pip.search_space.ProteomeSearchSpace attribute) (ms2pip.spectrum.ObservedSpectrum attribute) (ms2pip.spectrum.PredictedSpectrum attribute) (ms2pip.spectrum.Spectrum attribute) model_fields (ms2pip.result.ProcessingResult attribute) (ms2pip.search_space.ModificationConfig attribute) (ms2pip.search_space.ProteomeSearchSpace attribute) (ms2pip.spectrum.ObservedSpectrum attribute) (ms2pip.spectrum.PredictedSpectrum attribute) (ms2pip.spectrum.Spectrum attribute) ModificationConfig (class in ms2pip.search_space) module ms2pip ms2pip.correlation ms2pip.exceptions ms2pip.result ms2pip.search_space ms2pip.spectrum ms2pip.spectrum_input ms2pip.spectrum_output ms2pip module ms2pip command line option --logging-level --version -l ms2pip-annotate-spectra command line option --model --ms2-tolerance --output-name --processes --psm-filetype --spectrum-id-pattern -n -o -p -t PSMS SPECTRUM_FILE ms2pip-correlate command line option --add-ion-mobility --add-retention-time --compute-correlations --model --model-dir --ms2-tolerance --output-name --processes --psm-filetype --spectrum-id-pattern -i -n -o -p -r -t -x PSMS SPECTRUM_FILE ms2pip-get-training-data command line option --model --ms2-tolerance --output-name --processes --psm-filetype --spectrum-id-pattern -n -o -p -t PSMS SPECTRUM_FILE

ms2pip-predict-batch command line option --add-ion-mobility --add-retention-time --model --model-dir --output-format --output-name --processes --psm-filetype -f -i -n -o -r -t PSMS ms2pip-predict-library command line option --add-ion-mobility --add-retention-time --batch-size --config --model --model-dir --output-format --output-name --processes -c -f -i -n -o -r FASTA_FILE ms2pip-predict-single command line option --model --model-dir --output-format --output-name --plot -f -o -p PEPTIDOFORM ms2pip.constants.MODELS (built-in variable) ms2pip.correlation module ms2pip.exceptions module ms2pip.result module ms2pip.search_space module ms2pip.spectrum module ms2pip.spectrum_input module ms2pip.spectrum_output module ms2pip.spectrum_output.SUPPORTED_FORMATS (in module ms2pip.spectrum_output) ms2pip_pearson() (in module ms2pip.correlation) MS2PIPError MSP (class in ms2pip.spectrum_output)

N

NoMatchingSpectraFound

O

ObservedSpectrum (class in ms2pip.spectrum)

open() (ms2pip.spectrum_output.Bibliospec method) (ms2pip.spectrum_output.DLIB method)

P

PEPTIDOFORM ms2pip-predict-single command line option plot_spectra() (ms2pip.result.ProcessingResult method) predict_batch() (in module ms2pip) predict_library() (in module ms2pip) predict_single() (in module ms2pip) PredictedSpectrum (class in ms2pip.spectrum)

ProcessingResult (class in ms2pip.result) ProteomeSearchSpace (class in ms2pip.search_space) PSMS ms2pip-annotate-spectra command line option ms2pip-correlate command line option ms2pip-get-training-data command line option ms2pip-predict-batch command line option

R

read_spectrum_file() (in module ms2pip.spectrum_input)

remove_precursor() (ms2pip.spectrum.Spectrum method) remove_reporter_ions() (ms2pip.spectrum.Spectrum method)

S

spectral_angle() (in module ms2pip.correlation) Spectronaut (class in ms2pip.spectrum_output) Spectrum (class in ms2pip.spectrum)

SPECTRUM_FILE ms2pip-annotate-spectra command line option ms2pip-correlate command line option ms2pip-get-training-data command line option

T

tic (ms2pip.spectrum.Spectrum property) tic_norm() (ms2pip.spectrum.Spectrum method)

TitlePatternError to_spectrum_utils() (ms2pip.spectrum.Spectrum method) TSV (class in ms2pip.spectrum_output)

U

UnknownModelError UnknownOutputFormatError

UnresolvableModificationError UnsupportedSpectrumFiletypeError

W

write() (ms2pip.spectrum_output.Bibliospec method) (ms2pip.spectrum_output.DLIB method) (ms2pip.spectrum_output.MGF method) (ms2pip.spectrum_output.MSP method) (ms2pip.spectrum_output.Spectronaut method) (ms2pip.spectrum_output.TSV method)

write_correlations() (in module ms2pip.result) write_spectra() (in module ms2pip.spectrum_output)