spectral-data-loading-from-repository
Summary
Load tandem mass spectrometry (MS/MS) spectra from online proteomics and metabolomics repositories using Universal Spectrum Identifier (USI) strings, resolving repository accessions, file identifiers, and scan numbers to retrieve raw spectral data (m/z, intensity, precursor m/z, charge state, retention time) and instantiate MsmsSpectrum objects for downstream processing.
When to use
When you need to retrieve a specific MS/MS spectrum from a public proteomics repository (PRIDE, MassIVE, PeptideAtlas) by its USI string for annotation, visualization, or comparative analysis, rather than working with locally stored mzML/mzXML files or already-loaded spectrum objects.
When NOT to use
- Input spectra are already loaded locally as mzML/mzXML files or pre-instantiated MsmsSpectrum objects — use local file I/O instead.
- USI string is malformed or specifies a dataset that no longer exists or has restricted access.
- Batch loading of hundreds or thousands of spectra from a repository — consider downloading the raw dataset files directly for efficiency.
Inputs
- USI string (e.g., 'mzspec:MSV000082283:f07074:scan:5475')
- Online proteomics repository (PRIDE, MassIVE, PeptideAtlas)
Outputs
- MsmsSpectrum object with populated attributes (title, precursor m/z, charge, m/z array, intensity array, retention time)
How to apply
Parse the USI string (e.g., 'mzspec:PXD000561:Adult_Frontalcortex_bRP_Elite_85_f09:scan:17555') using spectrum_utils' USI resolver to extract the repository accession, dataset/file identifier, and scan number. Query the online proteomics resource endpoint via the USI mechanism to retrieve the raw spectrum data including m/z array, intensity array, precursor m/z, charge state, and retention time. Pass the resolved spectral attributes to the MsmsSpectrum constructor to instantiate a fully populated spectrum object. Verify that all required fields (title, precursor m/z, charge, m/z and intensity arrays) are accessible and non-empty before proceeding to processing steps such as mass range filtering, noise removal, or annotation.
Related tools
- spectrum_utils (Provides USI resolution, spectral data retrieval from online repositories, and MsmsSpectrum instantiation.) — https://github.com/bittremieux/spectrum_utils
- Python (Core language for implementing the spectrum loading workflow.)
- NumPy (Efficient array operations for storing and manipulating m/z and intensity arrays.) — https://www.numpy.org/
Examples
from spectrum_utils.spectrum import MsmsSpectrum; from spectrum_utils.utils import get_spectrum; usi = 'mzspec:PXD000561:Adult_Frontalcortex_bRP_Elite_85_f09:scan:17555'; spectrum = get_spectrum(usi)
Evaluation signals
- MsmsSpectrum object is successfully instantiated with non-null title, precursor_mz, charge, mz, and intensity attributes.
- m/z and intensity arrays have equal length and contain numeric values; m/z values are strictly increasing.
- Precursor m/z value matches the expected range for the specified ion type (e.g., singly to multiply charged ions).
- Retention time (if present in the repository) is a non-negative numeric value in seconds or minutes.
- Spectrum object can be serialized and passed to downstream processing functions (e.g., filter_intensity, annotate_proforma) without type errors.
Limitations
- USI resolution depends on network connectivity and repository endpoint availability; requests may fail or timeout if the repository is offline or throttles API traffic.
- Not all scan numbers or dataset accessions are guaranteed to exist or be publicly accessible; access may be restricted or data may have been withdrawn.
- Spectrum metadata (e.g., retention time, charge state) may be incomplete or absent in some repositories, resulting in partial MsmsSpectrum objects.
- Large or complex spectra may consume significant memory; batch loading without filtering can exhaust available RAM.
Evidence
- [other] Parse the USI string to extract repository accession, file/dataset identifier, and scan number using spectrum_utils' USI resolver.: "Parse the USI string to extract repository accession, file/dataset identifier, and scan number using spectrum_utils' USI resolver."
- [other] Retrieve the raw spectrum data (m/z array, intensity array, precursor m/z, charge state, retention time) from the online proteomics resource via the USI endpoint.: "Retrieve the raw spectrum data (m/z array, intensity array, precursor m/z, charge state, retention time) from the online proteomics resource (PRIDE, MassIVE, or equivalent) via the USI endpoint."
- [other] Instantiate an MsmsSpectrum object by passing the resolved spectrum data to the MsmsSpectrum constructor.: "Instantiate an MsmsSpectrum object by passing the resolved spectrum data (title, precursor m/z, charge, m/z array, intensity array, retention time) to the MsmsSpectrum constructor."
- [intro] Spectrum loading from online proteomics and metabolomics data resources using the Universal Spectrum Identifier (USI) mechanism.: "Spectrum loading from online proteomics and metabolomics data resources using the Universal Spectrum Identifier (USI) mechanism."
- [other] Load a spectrum from an online data resource by its Universal Spectrum Identifier (USI): "Load a spectrum from an online data resource by its Universal Spectrum Identifier (USI)"
1---2name: spectral-data-loading-from-repository3description: Use when when you need to retrieve a specific MS/MS spectrum from a public proteomics repository (PRIDE, MassIVE, PeptideAtlas) by its USI string for annotation, visualization, or comparative analysis, rather than working with locally stored mzML/mzXML files or already-loaded spectrum objects.4license: CC-BY-4.05---67# spectral-data-loading-from-repository89## Summary1011Load tandem mass spectrometry (MS/MS) spectra from online proteomics and metabolomics repositories using Universal Spectrum Identifier (USI) strings, resolving repository accessions, file identifiers, and scan numbers to retrieve raw spectral data (m/z, intensity, precursor m/z, charge state, retention time) and instantiate MsmsSpectrum objects for downstream processing.1213## When to use1415When you need to retrieve a specific MS/MS spectrum from a public proteomics repository (PRIDE, MassIVE, PeptideAtlas) by its USI string for annotation, visualization, or comparative analysis, rather than working with locally stored mzML/mzXML files or already-loaded spectrum objects.1617## When NOT to use1819- Input spectra are already loaded locally as mzML/mzXML files or pre-instantiated MsmsSpectrum objects — use local file I/O instead.20- USI string is malformed or specifies a dataset that no longer exists or has restricted access.21- Batch loading of hundreds or thousands of spectra from a repository — consider downloading the raw dataset files directly for efficiency.2223## Inputs2425- USI string (e.g., 'mzspec:MSV000082283:f07074:scan:5475')26- Online proteomics repository (PRIDE, MassIVE, PeptideAtlas)2728## Outputs2930- MsmsSpectrum object with populated attributes (title, precursor m/z, charge, m/z array, intensity array, retention time)3132## How to apply3334Parse the USI string (e.g., 'mzspec:PXD000561:Adult_Frontalcortex_bRP_Elite_85_f09:scan:17555') using spectrum_utils' USI resolver to extract the repository accession, dataset/file identifier, and scan number. Query the online proteomics resource endpoint via the USI mechanism to retrieve the raw spectrum data including m/z array, intensity array, precursor m/z, charge state, and retention time. Pass the resolved spectral attributes to the MsmsSpectrum constructor to instantiate a fully populated spectrum object. Verify that all required fields (title, precursor m/z, charge, m/z and intensity arrays) are accessible and non-empty before proceeding to processing steps such as mass range filtering, noise removal, or annotation.3536## Related tools3738- **spectrum_utils** (Provides USI resolution, spectral data retrieval from online repositories, and MsmsSpectrum instantiation.) — https://github.com/bittremieux/spectrum_utils39- **Python** (Core language for implementing the spectrum loading workflow.)40- **NumPy** (Efficient array operations for storing and manipulating m/z and intensity arrays.) — https://www.numpy.org/4142## Examples4344```45from spectrum_utils.spectrum import MsmsSpectrum; from spectrum_utils.utils import get_spectrum; usi = 'mzspec:PXD000561:Adult_Frontalcortex_bRP_Elite_85_f09:scan:17555'; spectrum = get_spectrum(usi)46```4748## Evaluation signals4950- MsmsSpectrum object is successfully instantiated with non-null title, precursor_mz, charge, mz, and intensity attributes.51- m/z and intensity arrays have equal length and contain numeric values; m/z values are strictly increasing.52- Precursor m/z value matches the expected range for the specified ion type (e.g., singly to multiply charged ions).53- Retention time (if present in the repository) is a non-negative numeric value in seconds or minutes.54- Spectrum object can be serialized and passed to downstream processing functions (e.g., filter_intensity, annotate_proforma) without type errors.5556## Limitations5758- USI resolution depends on network connectivity and repository endpoint availability; requests may fail or timeout if the repository is offline or throttles API traffic.59- Not all scan numbers or dataset accessions are guaranteed to exist or be publicly accessible; access may be restricted or data may have been withdrawn.60- Spectrum metadata (e.g., retention time, charge state) may be incomplete or absent in some repositories, resulting in partial MsmsSpectrum objects.61- Large or complex spectra may consume significant memory; batch loading without filtering can exhaust available RAM.6263## Evidence6465- [other] Parse the USI string to extract repository accession, file/dataset identifier, and scan number using spectrum_utils' USI resolver.: "Parse the USI string to extract repository accession, file/dataset identifier, and scan number using spectrum_utils' USI resolver."66- [other] Retrieve the raw spectrum data (m/z array, intensity array, precursor m/z, charge state, retention time) from the online proteomics resource via the USI endpoint.: "Retrieve the raw spectrum data (m/z array, intensity array, precursor m/z, charge state, retention time) from the online proteomics resource (PRIDE, MassIVE, or equivalent) via the USI endpoint."67- [other] Instantiate an MsmsSpectrum object by passing the resolved spectrum data to the MsmsSpectrum constructor.: "Instantiate an MsmsSpectrum object by passing the resolved spectrum data (title, precursor m/z, charge, m/z array, intensity array, retention time) to the MsmsSpectrum constructor."68- [intro] Spectrum loading from online proteomics and metabolomics data resources using the Universal Spectrum Identifier (USI) mechanism.: "Spectrum loading from online proteomics and metabolomics data resources using the Universal Spectrum Identifier (USI) mechanism."69- [other] Load a spectrum from an online data resource by its Universal Spectrum Identifier (USI): "Load a spectrum from an online data resource by its Universal Spectrum Identifier (USI)"
HolobiomicsLab 