spectrum_utils

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I am loading a spectrum by USI like this ``` usi = "mzspec:PXD031817:MSB19717Trypsin021915:scan:1930" spectrum = spectrum_utils.spectrum.MsmsSpectrum.from_usi(usi) ``` but I get this error: ``` Traceback (most recent call last): File "./plot-annotated-spectrum.py",...

wsnoble

Annotated sequence peptide string

15

[feature request] I was wondering if there is any desire to implement "adding the annotated ions on the peptide sequence string". "P]E]P]TIDEP[I[N[K" kind of deal ... like it is show...

jspaezp

Spectrum deisotoping based on the theoretical isotope intensity ratios by [Valkenborg et al. (2008)](http://link.springer.com/10.1016/j.jasms.2008.01.009). First, sequences of peaks at isotopic mass differences are identified. Next, the intensity ratios are compared...

bittremieux

Speedup of peptide parsing and annotation

1

This PR implements 4 main things, all with the purpose of improving speed of spectrum annotation workflows. 1. A fast-pass for unmodified peptides during the parsing. 2. The option for...

jspaezp

Noticed that `appdirs` is a depencency. This has been deprecated for a time now: https://github.com/ActiveState/appdirs?tab=readme-ov-file in favor of `platformdirs`: https://pypi.org/project/platformdirs/ They both have the same API so the migration should...

jspaezp

Get a less rounded mz_delta value in ppm for annotations?

1

Hi, thank you once again for this package. I am currently using it for some bulk annotations and, due to the rounding of ppm values to 1 decimal digit, I...

levitsky

annotate using custom fragment list

3

My peptide cannot be described with proforma. Does anyone have an example script of how to annotate from a custom table of fragments in tabular format ie (name,mz) ```import matplotlib.pyplot...

samcphee

Matplotlib Version

2

grid_b was deprecated in version >=3.7, causes an error. I was able to fix by pinning matplotlib to version 3.6.3

mwang87

function: noise peak removal

1

Hi Wout, Spectrum_utils is so powerful that I have completely switched to spectrum visualization using this tool. Spectrum_utils should be able to remove noise peaks, but I only see the...

danyunghsu

Update GNPS USI resolver to GNPS2

1

The [`GnpsBackend` should use](https://github.com/bittremieux/spectrum_utils/blob/main/spectrum_utils/spectrum.py#L15) `"https://metabolomics-usi.gnps2.org/proxi/v{version}/spectra?usi={usi}"` now.

bittremieux