Command line interface

ms2pip

ms2pip [OPTIONS] COMMAND [ARGS]...

Options

-l, --logging-level <logging_level>

Options:: DEBUG | INFO | WARNING | ERROR | CRITICAL

--version: Show the version and exit.

annotate-spectra

Annotate observed spectra.

Parameters

psms: PSMList or path to PSM file that is supported by psm_utils.
spectrum_file: Path to spectrum file with target intensities.
psm_filetype: Filetype of the PSM file. By default, None. Should be one of the supported psm_utils filetypes. See https://psm-utils.readthedocs.io/en/stable/#supported-file-formats.
spectrum_id_pattern: Regular expression pattern to apply to spectrum titles before matching to peptide file spec_id entries.
model: Model to use as reference for the ion types that are extracted from the observed spectra. Default: “HCD”, which results in the extraction of singly charged b- and y-ions.
ms2_tolerance: MS2 tolerance in Da for observed spectrum peak annotation. By default, 0.02 Da.
processes: Number of parallel processes for multiprocessing steps. By default, all available.

Returns

results: List[ProcessingResult]: List of ProcessingResult objects with theoretical m/z and observed intensity values.

ms2pip annotate-spectra [OPTIONS] PSMS SPECTRUM_FILE

Options

-t, --psm-filetype <psm_filetype>

Options:: idxml | msms | mzid | peprec | pepxml | percolator | proteome_discoverer | timscore | tsv | xtandem | msamanda | sage | ionbot

-o, --output-name <output_name>

-p, --spectrum-id-pattern <spectrum_id_pattern>

--model <model>

Options:: CID | HCD2019 | TTOF5600 | TMT | iTRAQ | iTRAQphospho | HCDch2 | CIDch2 | HCD2021 | Immuno-HCD | CID-TMT | timsTOF2023 | timsTOF2024 | HCD | timsTOF

--ms2-tolerance <ms2_tolerance>

-n, --processes <processes>

Arguments

PSMS: Required argument

SPECTRUM_FILE: Required argument

correlate

Compare predicted and observed intensities and optionally compute correlations.

Parameters

psms: PSMList or path to PSM file that is supported by psm_utils.
spectrum_file: Path to spectrum file with target intensities.
psm_filetype: Filetype of the PSM file. By default, None. Should be one of the supported psm_utils filetypes. See https://psm-utils.readthedocs.io/en/stable/#supported-file-formats.
spectrum_id_pattern: Regular expression pattern to apply to spectrum titles before matching to peptide file spec_id entries.
compute_correlations: Compute correlations between predictions and targets.
add_retention_time: Add retention time predictions with DeepLC (Requires optional DeepLC dependency).
model: Model to use for prediction. Default: “HCD”.
model_dir: Directory where XGBoost model files are stored. Default: ~/.ms2pip.
ms2_tolerance: MS2 tolerance in Da for observed spectrum peak annotation. By default, 0.02 Da.
processes: Number of parallel processes for multiprocessing steps. By default, all available.

Returns

results: List[ProcessingResult]: Predicted spectra with theoretical m/z and predicted intensity values, and optionally, correlations.

ms2pip correlate [OPTIONS] PSMS SPECTRUM_FILE

Options

-t, --psm-filetype <psm_filetype>

Options:: idxml | msms | mzid | peprec | pepxml | percolator | proteome_discoverer | timscore | tsv | xtandem | msamanda | sage | ionbot

-o, --output-name <output_name>

-p, --spectrum-id-pattern <spectrum_id_pattern>

-x, --compute-correlations

-r, --add-retention-time

--model <model>

Options:: CID | HCD2019 | TTOF5600 | TMT | iTRAQ | iTRAQphospho | HCDch2 | CIDch2 | HCD2021 | Immuno-HCD | CID-TMT | timsTOF2023 | timsTOF2024 | HCD | timsTOF

--model-dir <model_dir>

--ms2-tolerance <ms2_tolerance>

-n, --processes <processes>

Arguments

PSMS: Required argument

SPECTRUM_FILE: Required argument

get-training-data

Extract feature vectors and target intensities from observed spectra for training.

Parameters

psms: PSMList or path to PSM file that is supported by psm_utils.
spectrum_file: Path to spectrum file with target intensities.
psm_filetype: Filetype of the PSM file. By default, None. Should be one of the supported psm_utils filetypes. See https://psm-utils.readthedocs.io/en/stable/#supported-file-formats.
spectrum_id_pattern: Regular expression pattern to apply to spectrum titles before matching to peptide file spec_id entries.
model: Model to use as reference for the ion types that are extracted from the observed spectra. Default: “HCD”, which results in the extraction of singly charged b- and y-ions.
ms2_tolerance: MS2 tolerance in Da for observed spectrum peak annotation. By default, 0.02 Da.
processes: Number of parallel processes for multiprocessing steps. By default, all available.

Returns

features: pandas.DataFrame with feature vectors and targets.

ms2pip get-training-data [OPTIONS] PSMS SPECTRUM_FILE

Options

-t, --psm-filetype <psm_filetype>

Options:: idxml | msms | mzid | peprec | pepxml | percolator | proteome_discoverer | timscore | tsv | xtandem | msamanda | sage | ionbot

-o, --output-name <output_name>

-p, --spectrum-id-pattern <spectrum_id_pattern>

--model <model>

Options:: CID | HCD2019 | TTOF5600 | TMT | iTRAQ | iTRAQphospho | HCDch2 | CIDch2 | HCD2021 | Immuno-HCD | CID-TMT | timsTOF2023 | timsTOF2024 | HCD | timsTOF

--ms2-tolerance <ms2_tolerance>

-n, --processes <processes>

Arguments

PSMS: Required argument

SPECTRUM_FILE: Required argument

predict-batch

Predict fragmentation spectra for a batch of peptides.

Parameters

psms: PSMList or path to PSM file that is supported by psm_utils.
psm_filetype: Filetype of the PSM file. By default, None. Should be one of the supported psm_utils filetypes. See https://psm-utils.readthedocs.io/en/stable/#supported-file-formats.
add_retention_time: Add retention time predictions with DeepLC (Requires optional DeepLC dependency).
model: Model to use for prediction. Default: “HCD”.
model_dir: Directory where XGBoost model files are stored. Default: ~/.ms2pip.
processes: Number of parallel processes for multiprocessing steps. By default, all available.

Returns

predictions: List[ProcessingResult]: Predicted spectra with theoretical m/z and predicted intensity values.

ms2pip predict-batch [OPTIONS] PSMS

Options

-o, --output-name <output_name>

-f, --output-format <output_format>

Options:: csv | mgf | msp | bibliospec | spectronaut | dlib

-r, --add-retention-time

--model <model>

Options:: CID | HCD2019 | TTOF5600 | TMT | iTRAQ | iTRAQphospho | HCDch2 | CIDch2 | HCD2021 | Immuno-HCD | CID-TMT | timsTOF2023 | timsTOF2024 | HCD | timsTOF

--model-dir <model_dir>

-n, --processes <processes>

Arguments

PSMS: Required argument

predict-library

Predict spectral library from protein FASTA file.

ms2pip predict-library [OPTIONS]

predict-single

Predict fragmentation spectrum for a single peptide.

ms2pip predict-single [OPTIONS] PEPTIDOFORM

Options

-o, --output-name <output_name>

--model <model>

Options:: CID | HCD2019 | TTOF5600 | TMT | iTRAQ | iTRAQphospho | HCDch2 | CIDch2 | HCD2021 | Immuno-HCD | CID-TMT | timsTOF2023 | timsTOF2024 | HCD | timsTOF

--model-dir <model_dir>

-p, --plot

Arguments

PEPTIDOFORM: Required argument