mobiusklein
commented
5 years ago Thank you for your interest in my work. I'm glad it's (partially) helping you.
Saving Spectra
If I'm following your post correctly, you started with an input MS data file of some sort (another mzML file?) with only MS2 spectra, and attempting to export the processed spectra did not work as expected because the save_scan_bunch method expected a precursor?
This sounds like a combination of things weren't aligned. The mzML format supports MS2-only files and the readers and writers in ms_deisotope should too.
When you iterated over your input file, were you getting Scan or ScanBunch instances? A Scan is a single scan/spectrum, while a ScanBunch is a collection of an MS1 scan (which may be None) and zero or more MSn scans. Since you have a snippet invoking bunch.deconvolute, and only Scan objects have a deconvolute method, I assume bunch is a Scan. MzMLSerializer.save_scan_bunch assumes its input is a ScanBunch. To save a single Scan, you should call MzMLSerializer.save_scan, or you can use the MzMLSerializer.save method, which does type checking to figure out which method to use. In the docs, I show an example using save.
I probably need to document the iteration modes better, since it sounds like you've read some examples where iteration yields ScanBunch instances, but that didn't match what you had.
The mzML snippet you posted appears to be missing the <precursorList> element. Is it present in your input file? I can't tell if this is because you've changed the scan saving code, or because it is missing. if you can share the file, I might be able to better understand what's happening.
What Is Saved
When you save a deconvoluted scan with ms_deisotope's MzMLSerializer, your <spectrum> elements contain the following <binaryDataArray>s:
- m/z array - The monoisotopic m/z of each deconvoluted peak, given by their neutral mass and charge state
- intensity array - The sum of the intensity of all isotopic peaks underlying each deconvoluted peak
- charge array - The charge state of the ion forming the isotopic pattern underlying each deconvoluted peak
- deconvolution score array - Non-standard. The score of the theoretical isotopic pattern fit underlying each deconvoluted peak
- isotopic envelope array - Non-standard. The isotopic peaks of each deconvoluted peak. This array is a bit tricky to decode. All of the previous arrays map a single value to each peak, where this array maps a variable number of values to each peak. Every two values in this array correspond to the m/z and intensity of an isotopic peak, and distinct isotopic patterns are delimited by a pair of 0 entries. See the following function from
ms_deisotope.output.text_utilsfor the implementation:def decode_envelopes(array): envelope_list = [] current_envelope = [] i = 0 n = len(array) while i < n: a = array[i] b = array[i + 1] i += 2 if a == 0 and b == 0: if current_envelope is not None: if current_envelope: envelope_list.append(Envelope(current_envelope)) current_envelope = [] else: current_envelope.append(EnvelopePair(a, b)) envelope_list.append(Envelope(current_envelope)) return envelope_listThis lets me reconstruct
DeconvolutedPeakinstances, preserving theirenvelopeattributes which is where the experimental isotopic patterns get stored. This hopefully takes care of encoding the isotopic patterns for you as well. Note, they are at whatever charge state the matching deconvoluted peak was fit at.
You said you'd prefer for the m/z stored to be de-charged, so transformed as if z = 1. I don't have a method for doing that directly, but while I figure out if there is a better way, you could just do the following to achieve the desired effect:
import ms_deisotope
for peak in scan.deconvoluted_peak_set:
peak.mz = ms_deisotope.mass_charge_ratio(peak.neutral_mass, 1)
peak.charge = 1
scan.deconvoluted_peak_set.reindex()
JeffEdge
Thank you for this fantastic library. Briefly what works:
What I have issues with is exporting a mzML file of the deconvoluted data. While my knowledge of mzML is limited I tried the following to address the fact that I have no MS1 scan and no precursor list (the graphical output seems to work so I focused on the writer part)
Where save_scan_bunch2() is a method where I edited "precursor" out:
In save_scan2(), I just commented out the bloc staring with
if scan.precursor_information:Now my problems really start: The edited add_scan_bunch() so that add_scan_bunch2() looks like
All this yields a mzML file which displays using openMS as centroided deisotope peaks ( nothing else), see file at the end.
First I believe I might have an indexation problem but I am not sure. Could it be that the issue stems from the binaryDataArrayList breaking the data into 5 parts.
Ultimately what I would like is export a charge deconvoluted spectrum (everything converted to MH+ ions, no higher charge states) and if possible a list of the isotope distributions extracted (ideally MH+) also. Perhaps it would be possible to create a new method to export an extracted isotope distribution and find a way to append them in a single mzML file?
Any help would be very much appreciated! Many thanks, With my best wishes, Jeff
If it is any help I can provide a MS2 single scan data file. The output written out is below.