ms2pip.spectrum_output

Write spectrum files from MS²PIP prediction results.

Examples

The simplest way to write MS²PIP predictions to a file is to use the write_spectra() function:

>>> from ms2pip import predict_single, write_spectra
>>> results = [predict_single("ACDE/2")]
>>> write_spectra("/path/to/output/filename", results, "mgf")

Specific writer classes can also be used directly. Writer classes should be used in a context manager to ensure the file is properly closed after writing. The following example writes MS²PIP predictions to a TSV file:

>>> from ms2pip import predict_single
>>> results = [predict_single("ACDE/2")]
>>> with TSV("output.tsv") as writer:
...     writer.write(results)

Results can be written to the same file sequentially:

>>> results_2 = [predict_single("PEPTIDEK/2")]
>>> with TSV("output.tsv", write_mode="a") as writer:
...     writer.write(results)
...     writer.write(results_2)

Results can be written to an existing file using the append mode:

>>> with TSV("output.tsv", write_mode="a") as writer:
...     writer.write(results_2)

ms2pip.spectrum_output.write_spectra(filename, processing_results, file_format='tsv', write_mode='w')[source]

Write MS2PIP processing results to a supported spectrum file format.

Parameters:

filename (str | Path) – Output filename without file extension.
processing_results (List[ProcessingResult]) – List of ms2pip.result.ProcessingResult objects.
file_format (str) – File format to write. See FILE_FORMATS for available formats.
write_mode (str) – Write mode for file. Default is w (write). Use a (append) to add to existing file.

class ms2pip.spectrum_output.TSV(filename, write_mode='w')[source]

Bases: _Writer

Write TSV files from MS2PIP processing results.

Parameters:

filename (Union[str, Path]) –
write_mode (str) –

write(processing_results)[source]

Write multiple processing results to file.

Parameters:: processing_results (List[ProcessingResult]) –

class ms2pip.spectrum_output.MSP(filename, write_mode='w')[source]

Bases: _Writer

Write MSP files from MS2PIP processing results.

Parameters:

filename (Union[str, Path]) –
write_mode (str) –

write(results)[source]

Write multiple processing results to file.

Parameters:: results (List[ProcessingResult]) –

class ms2pip.spectrum_output.MGF(filename, write_mode='w')[source]

Bases: _Writer

Write MGF files from MS2PIP processing results.

See http://www.matrixscience.com/help/data_file_help.html for documentation on the MGF format.

Parameters:

filename (Union[str, Path]) –
write_mode (str) –

write(results)[source]

Write multiple processing results to file.

Parameters:: results (List[ProcessingResult]) –

class ms2pip.spectrum_output.Spectronaut(filename, write_mode='w')[source]

Bases: _Writer

Write Spectronaut files from MS2PIP processing results.

Parameters:

filename (Union[str, Path]) –
write_mode (str) –

write(processing_results)[source]

Write multiple processing results to file.

Parameters:: processing_results (List[ProcessingResult]) –

class ms2pip.spectrum_output.Bibliospec(filename, write_mode='w')[source]

Bases: _Writer

Write Bibliospec SSL and MS2 files from MS2PIP processing results.

Bibliospec SSL and MS2 files are also compatible with Skyline. See https://skyline.ms/wiki/home/software/BiblioSpec/page.view?name=BiblioSpec%20input%20and%20output%20file%20formats for documentation on the Bibliospec file formats.

Parameters:

filename (Union[str, Path]) –
write_mode (str) –

open()[source]: Open files.

close()[source]: Close files.

write(processing_results)[source]

Write multiple processing results to file.

Parameters:: processing_results (List[ProcessingResult]) –

class ms2pip.spectrum_output.DLIB(filename, write_mode='w')[source]

Bases: _Writer

Write DLIB files from MS2PIP processing results.

See EncyclopeDIA File Formats for documentation on the DLIB format.

Parameters:

filename (Union[str, Path]) –
write_mode (str) –

open()[source]: Open file.

write(processing_results)[source]

Write MS2PIP predictions to a DLIB SQLite file.

Parameters:: processing_results (List[ProcessingResult]) –

ms2pip.spectrum_output.SUPPORTED_FORMATS: dict: Supported file formats and respective _Writer class for spectrum output.