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Scoring spectra with HyperScore | ||
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In the chapter on spectrum alignment we showed how to determine matching peaks between theoretical and experimental spectra. | ||
For many use cases we might actually not be interested in obtaining the list of matched peaks but would like to have | ||
a simple, single score that indicates how "well" the two spectra matched. | ||
The HyperScore is a method to assign a spectrum match score to spectrum matches. | ||
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Background | ||
********** | ||
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HyperScore computes the (ln transformed) X!Tandem HyperScore of theoretical spectrum, | ||
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calculated from a peptide/oligonucleotide sequence, with an experimental spectrum, | ||
loaded from an mzML file. | ||
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1. the dot product of peak intensities between matching peaks in experimental and theoretical spectrum is calculated | ||
2. the HyperScore is calculated from the dot product by multiplying by factorials of matching b- and y-ions | ||
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.. code-block:: python | ||
from urllib.request import urlretrieve | ||
from pyopenms import * | ||
gh = "https://raw.githubusercontent.com/OpenMS/pyopenms-docs/master" | ||
urlretrieve(gh + "/src/data/SimpleSearchEngine_1.mzML", "searchfile.mzML") | ||
Generate a theoretical spectrum | ||
******************************* | ||
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We now use the TheoreticalSpectrumGenerator to generate a theoretical spectrum for the sequence we are interested in, | ||
``RPGADSDIGGFGGLFDLAQAGFR``, and compare the peaks to a spectra from our file. | ||
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.. code-block:: python | ||
tsg = TheoreticalSpectrumGenerator() | ||
thspec = MSSpectrum() | ||
p = Param() | ||
p.setValue("add_metainfo", "true") | ||
tsg.setParameters(p) | ||
peptide = AASequence.fromString("RPGADSDIGGFGGLFDLAQAGFR") | ||
tsg.getSpectrum(thspec, peptide, 1, 1) | ||
# Iterate over annotated ions and their masses | ||
for ion, peak in zip(thspec.getStringDataArrays()[0], thspec): | ||
print(ion, peak.getMZ()) | ||
e = MSExperiment() | ||
MzMLFile().load("searchfile.mzML", e) | ||
spectrum_of_interest = e[2] | ||
print("Spectrum native id", spectrum_of_interest.getNativeID()) | ||
mz, i = spectrum_of_interest.get_peaks() | ||
peaks = [(mz, i) for mz, i in zip(mz, i) if i > 1500 and mz > 300] | ||
for peak in peaks: | ||
print(peak[0], "mz", peak[1], "int") | ||
Comparing the theoretical spectrum and the experimental spectrum for | ||
``RPGADSDIGGFGGLFDLAQAGFR`` we can easily see that the most abundant ions in the | ||
spectrum are y8 (877.452 m/z), b10 (926.432), y9 (1024.522 m/z) and b13 | ||
(1187.544 m/z). | ||
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Getting a score | ||
*************** | ||
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We now run HyperScore to compute the similarity of the theoretical spectrum | ||
and the experimental spectrum and print the result | ||
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.. code-block:: python | ||
hscore = HyperScore() | ||
fragment_mass_tolerance = 5.0 | ||
is_tol_in_ppm = True | ||
result = hscore.compute(fragment_mass_tolerance, is_tol_in_ppm, spectrum_of_interest, thspec) | ||
result | ||
If we didn't know ahead of time which spectrum was a match we can loop through all the spectra from our file, | ||
calculate scores for all of them, and print the result: | ||
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.. code-block:: python | ||
for f in e: | ||
score = hscore.compute(fragment_mass_tolerance, is_tol_in_ppm, f, thspec) | ||
print(f.getNativeID() + ":" + str(score)) | ||