Table of Contents

Display utility for 2D FTICR Spectra

This little utility allows to interactively explore large 2D FTICR-MS datasets.

You find here a simple interface the reads and displays the multiresolution 2D files created by SPIKE when processing 2D data-sets (usually called xxx_mr.msh5).

It is based on the capabilities of both the SPIKE library and the jupyter notebook interface. Thanks to the technology behind, these extremely large files can be accessed rapidly, even on a laptop computer.

This program supersedes the old Visu2D program, developped in Qt, which could no longer be maintained.

This is a work inprogress - additional utilities should come soon !

To use it,

execute each executable cell (marked with the In[]) either by cliking on the Run icon on the top of the window, or by hitting shift-Return on the keyboard

Initialization of the environment

the following cell should be run only once, at the beginning of the processing

In [1]:
from IPython.display import display, HTML, Markdown, Image
display(Markdown('## STARTING Environment...'))
%matplotlib notebook
import spike.Interactive.INTER as I
from spike.Interactive.FTICR_INTER import MR, MR_interact
from spike.Interactive.ipyfilechooser import FileChooser
I.hidecode()

STARTING Environment...

    ========================
          SPIKE
    ========================
    Version     : 0.99.12
    Date        : 11-09-2019
    Revision Id : 425
    ========================
*** zoom3D not loaded because of an error ***
plugins loaded:
Bruker_NMR_FT,  Bucketing,  FTMS_calib,  Fitter,  Integrate,  Linear_prediction,  PALMA,  Peaks,  apmin,  bcorr,  bokeh_display,  fastclean,  gaussenh,  pg_sane,  rem_ridge,  sane,  sg,  test,  urQRd,  wavelet, 

spike.plugins.report() for a short description of each plugins
spike.plugins.report('module_name') for complete documentation on one plugin
usefull to show/print a clean screen when processing is finished

Choose the file

Use FileChooser() to choose a file on your disk - The optional base argument, starts the exploration on a given location.

2D processed files are *.msh5 files.

In [2]:
FC = FileChooser('/DATA',filetype='y*.msh5', mode='r')
display(FC)

the MR tool simply loads and describe the content of the file

In [ ]:
MR(FC.selected)

MR_interact loads and display the data-set.

It can be called directly

In [3]:
MR_interact(FC.selected);

/DATA/pour Florence/yeast_extract_p9kk_dn200_small_mr.msh5
2D data-set
Axis F1 :FT-ICR report axis at 500.000000 kHz,  4096 real points,  from physical mz =  328.280   to m/z = 3000.000  R max (M=400) = 3774
Axis F2: FT-ICR report axis at 1250.000000 kHz,  262144 real points,  from physical mz =  147.412   to m/z = 3000.000  R max (M=400) = 96608
data-set is real
=====================
multiresolution data:
#: Size
1: 4096 x 262144 : 1024 Mpix
2: 1024 x 65536 : 64 Mpix
3: 1024 x 16384 : 16 Mpix
4: 1024 x 4096 : 4 Mpix
5: 1024 x 1024 : 1 Mpix
  • 🔍 in : zoom win
  • 🔍out : zoom out
  • ◀︎ : moves the zoom window left
  • ▶︎ : moves the zoom window right
  • ▲ : moves the zoom window up
  • ▼ : moves the zoom window down
  • ⍇ : back in zoom list
  • ⍈ : forward in zoom list
  • you can also directly enter the zoom coordinates, the click on Update
  • × : lower the levels used for the display
  • ÷ : raise the levels used for the display
  • ≡ : reset default levels
  • ⌘ : reset to initial view

Note that the 2D files contain several version of the spectrum at different resolution - zooming and out may modify the look of the region you are looking to. Only the closest zoom contains the unbiaised verion of the spectrum.

Some additional options are possible:

  • store the view into a python variable (we'll see other usage below)
  • store the created view into a python variable
  • define behaviour at start-up
  • overload the initial view
In [4]:
# complete initialisation, and storing the view into a python var
DI = MR_interact(FC.selected,
                report=False,   # inhibits parameter printing
                show=False,     # does not display on start-up
                figsize=(15,15),# Size of initial display (in cm)
                Debug=False     # Enables live debugging if True
               )
DI._zoom = (380, 700, 380, 700)     # set the initial zoom view, in m/z (F1low , F1High , F2low , F2High)
DI.scale = 3.0                      # set the initial scale
DI.show()                           # and finally show

/DATA/pour Florence/yeast_extract_p9kk_dn200_small_mr.msh5

There is 1D extraction tool which is handy to examine carefully the details

Just use your stored view and append .I1D() to it

In [5]:
DI.I1D()

to come

  • calibration
  • peak detection
  • superimposition
  • exctaction of arbitrary 1D
  • locate artifacts due to harmonics
In [ ]: