jamesetsmith/msanalysis

Python Tools for Mass Spec. Analysis

msanalysis's Issues

could not broadcast input array (aka empty MS scan in mzXML file)

Problem Description

Traceback (most recent call last):
  File "/Users/ann.lii.rosales/Desktop/Python/msanalysis/examples/05_relative_abundance.py", line 41, in <module>
    data = read_mzXML(mzXML_file)
  File "/Users/ann.lii.rosales/Desktop/Python/msanalysis/msanalysis/data_extraction/utils.py", line 125, in read_mzXML
    intensities[i] = s.get_peaks()[1]
ValueError: could not broadcast input array from shape (0) into shape (26947)

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Steps to Reproduce

I modified example 5 to plot data from the real mzXML file (which we now know is corrupted/problematic) and ran the example:

bash python 05_relative_abundance.py

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Expected/Desired Behaviour

The corrupted mzXML files is beyond our control, but we need a more descriptive error message when this happens in the future.

Generate MS fingerprint for molecule

Given a molecular formular we want to generate a mass spec. fingerprint.

Travis CI Security Breach Notice

MolSSI is reaching out to every repository created from the MolSSI Cookiecutter-CMS with a .travis.yml file present to alert them to a potential security breach in using the Travis-CI service.

Between September 3 and September 10 2021, the Secure Environment Variables Travis-CI uses were leaked for ALL projects and injected into the publicly available runtime logs. See more details here. All Travis-CI users should cycle any secure variables/files, and associated objects as soon as possible. We are reaching out to our users in the name of good stewards of the third-party products we recommended and might still be in use and provide a duty-to-warn to our end-users given the potential severity of the breach.

We at MolSSI recommend moving away from Travis-CI to another CI provider as soon as possible. The nature of this breach and the way the response was mis-handled by Travis-CI, MolSSI cannot recommend the Travis-CI platform for any reason at this time. We suggest either GitHub Actions (as is used from v1.5 of the Cookiecutter-CMS) or some other service offered on GitHub.

If you have already addressed this security concern or it does not apply to you, feel free to close this issue.

This issue was created programmatically to reach as many potential end-users as possible. We do apologize if this was sent in error.

ex6: missing isotope for Ge

ex6_iso_abundancy is missing an isotopic abundance for Germanium (Ge). According to this website (https://www.sisweb.com/mstools/isotope.htm), Ge has an abundance at 76 amu. However, ex6 does not display 76 amu (the plot stops at 74 amu; please see attached). Not sure if the data base needs to updated.

Add ability to read from txt file

Convert non-uniform spectral data storage to uniform (np.ndarray) storage

Since the actual data from the MS is uniform, unlike what we were seeing in the CDF outputs, we should stop storing the spectral data as lists and use numpy arrays to simplify code and speed things up.

Peak detection/fitting and deconvolution

• Peak detection/fitting would help speed up QMS data analysis immensely. This would include generating isotope patterns based on possible etch products. Then, fitting would entail fitting the calculated patterns to the experimental data. Fitting output would include quality of fitting (eg, percent match to the isotope fingerprints).

• Peak deconvolution would help identify species with overlapping m/z values. Deconvolution would involve linear combination of relative peak intensities from different species.

Peak loss in log-scale contour plots

Low intensity peaks don't show up in the current log scale contour plots (example 4). One resolution would be to remove the intense bands from precursor that are present throughout the temperature ramp. This requires input of m/z ranges of the intense bands that the users wish to exclude in the codes. Hopefully this will allow the low intensity peaks to show.