jbellamycarter / pepfoot Goto Github PK

The release update checker added to v1.2.0 causes pepFoot to crash when there is poor connectivity.

Importing .mz5 converted from Bruker instruments (via .mzXML intermediate) fails with an error like so:

Traceback (most recent call last):
File "pepFoot\pepFootGui.py", line 848, in update_PepList
File "pepFoot\pepFootGui.py", line 314, in wrapper
File "pepFoot\pepFootGui.py", line 776, in file_import
File "pepFoot\pepFootGui.py", line 785, in open_mz5
File "pepFoot\mz5Reader.py", line 61, in __init__
File "h5py\_objects.pyx", line 54, in h5py._objects.with_phil.wrapper
File "h5py\_objects.pyx", line 55, in h5py._objects.with_phil.wrapper
File "site-packages\h5py\_hl\group.py", line 177, in __getitem__
File "h5py\_objects.pyx", line 54, in h5py._objects.with_phil.wrapper
File "h5py\_objects.pyx", line 55, in h5py._objects.with_phil.wrapper
File "h5py\h5o.pyx", line 190, in h5py.h5o.open
KeyError: "Unable to open object (object 'ChromatogramIndex' doesn't exist)"

This is caused by Bruker data files lacking a discrete total ion chromatogram, which is required to generate ChromatogramIndex and related structures in .mz5 files. PepFoot uses this entry to determine the number of scans in the data file, which are subsequently used for filling a lookup table.

As described in the original PepFoot paper¹ (see Figure S1, pasted below), occasionaly instability in FT instruments (such as FT-ICR or Orbitrap) can lead to slight shifts in recorded m/z and therefore apparent peak splitting when processed in PepFoot; this is not seen in Xcalibur as the spectra are summed to a tolerance (essentially interpolated). This makes viewing for users very difficult, especially if a common occurance in data files.

🔨 Suggested Enhancement: Change spectrum viewer to display an interpolated spectrum, this should not affect integration.

Currently the GUI limits max. missed cleavages to 3. For most proteases this is okay but pepsin and similar promiscuous proteases generate peptides that may have many more than this.

Combining spectra which are empty in th emz region of interest (particularly when these where then being peak detected) gives an empty array error, (line 1111). Error spotted by James.

Hi Jed,

Is there any chance that in a future version of PepFoot you could include a Y-Axis Zoom on the Spectrum?

When I have two overlaying spectra, like in the example attached, my peaks of interest are swamped by the higher intensity peaks. Therefore I have to zoom in on each peak individually in the X direction to check the mass error, and its difficult to gauge whether the predicted distribution fits the actual distribution.

Cheers
Harry