Update to ORIGAMI-ANALYSE (1.0.1)

What changed in ORIGAMI^ANALYSE :

Fixes in v1.0.1:

• fixed an issue where images were not saved properly (i.e. when you right-clicked in the document panel and selected 'Save figure')
• fixed some issues in the CCS calibration panel
• fixed an issue in the RMSD label positioning (i.e. when the Y-axis/X-axis values didn't start at 0/1)

New in v1.0.1: 

• added several new shortcut keys to make analysis a little easier
  • Alt+E now extracts all ions from the Peak list
  • Alt+Q and Alt+W now overlay 2D plots (Q = ions; W = text files)
  • Alt+S now plots currently selected item in the 'Documents Panel'
  • Alt+D now adds new 'Comparison document'
• 1D and RT overlay plots will now be added to the 'Comparison document' and can be easily visualised by right-clicking on the item and selecting 'Show'
• You can now load-in CCS calibration database (Ctrl+Alt+C) and show it (Ctrl+Shift+C) and assign an item from the database to an item in the calibration window
• You can also use the same CCS calibration database to add your most commonly used proteins/molecules and quickly assign them to a loaded file (through 'Notes, Information, Labels...')
• Added CCS calibration information panel to the 'Notes, Information, Labels...' panel accessible from the 'Documents Panel'
• You can now make your RMSD label bold 
• You can now rename (some!) items in the 'Documents Panel' by right-clicking on the item and selecting option: 'Rename'

Known issues:

• The DT-IMS panel still lacks a lot of functions
• The 3D plot can be improved a lot, just need a bit of time to tinker!
• The GUI needs some restructuring

Video tutorials:

Released first video about how to setup ORIGAMI^MS! A couple more are coming in the next few days from the same YouTube channel. 

ORIGAMI-MS: Setup Guide

Documentation

Have been pre-occupied with other things but made some changes to the User Guides. They still require a lot of work but hopefully few things are a little more clear! :)

How to update

If you already have ORIGAMI on your PC, then all you have to do is download the updateFilesOnly_ORIGAMI_ANALYSE_v1.0.1.zip file, extract it and copy the contents to the ORIGAMI^ANALYSE folder. 

If you do now, just download the ORIGAMI_ANALYSE_v1.0.1.zip, unpack it somewhere on your PC and you are good to go! :)

 

Thanks,

Lukasz

 

ORIGAMI (1.0.0)

An initial release of ORIGAMI^MS  and ORIGAMI^ANALYSE ! 

ORIGAMI is designed to provide intuitive graphical interface for routine analysis of mass spectrometry and ion mobility mass spectrometry datasets. The program was designed with activated IM-MS (or CIU) datasets in mind, in particular to speed up the extraction of data, processing and improve the visualisation methods that are currently available.

First, let's start off with ORIGAMI^MS :

Current version: 1.0.2

In this version, you are able to perform collisional activation ramp on Waters Synapt G2/G2S and G2Si instruments in the trap collision cell or in the sample cone in either positive or negative ionisation mode. The gradient of the ramp is determined by the provided parameters. Currently there are four available methods which include: linear, exponential, Boltzmann and User-defined. These differ quite significantly from one another, so if you would like more information, please refer to the publication or the User Guide. 

 There are a couple of requirements for the program to run:

1. You will need an ion mobility instrument: Synapt G2/G2S or G2Si
2. Installed WREnS. I have been using version 2.15.7 but older versions should work too (it just needs to have the mini-program ScriptRunnerLight.exe
3. Driftscope and ORIGAMI^ANALYSE to analyse your data

 Main features:

• Clean and simple to use GUI
• Simplified and speed-up acquisition of activated IM-MS/CIU datasets
• Selection of built-in methods to perform collisional activation
• Allows activation in the sample cone or trap collision cell
• Works in both positive and negative mode
• Easy to analyse in ORIGAMI^ANALYSE

 Now, ORIGAMI^ANALYSE:   

 Current version: 1.0.0

In this initial release, you are able to perform direct analysis of MassLynx files, either in a single or batch modes. The program works pretty well to automate and simplify a lot of tedious tasks, i.e. extracting and forming 2D arrays. For the time being, ORIGAMI^ANALYSE can analyse text and MassLynx files only.  

The only requirement for the program to work is a local installation of Driftscope and that it is run on a 64bit Windows 7/8/10 machine.

Main features:

• Allows direct analysis of single or multiple ORIGAMI^MS files
• Speeds-up your analysis process by simplifying processing of manually acquired aIM-MS datasets (CIU, SID, ERMS…)
• Easy to use extraction tools for single or multiple MassLynx files
• Easy to maintain project files – saves all your data (MS, RT, 1D, 2D…) in one place which you can share with colleagues or come back to it later
• Lots of visualisation options to stylise your aIM-MS plots
• Comprehensive comparison tools with mask, transparent, RMSD, RMSF and many other plot types
• Export all your data in an interactive format and share it with the community
• Save all your data in text format
• Save each figure in your desired format

Still under development:

• The CCS calibration has not been fully optimised yet and several features have been disabled as they were causing issues - working on a fix and will update soon
• The Drtift-Time panel is very much under-developed and is missing a lot of features - it aims to simplify analysis of WREnS acquired DT-IMS datasets (not released yet)

Apart from that, most other features should work as intended (should is the key word here).

I am currently writing comprehensive guides, as I am aware there might be a lot of features and buttons in the GUI! I will be updating it frequently on GitHub. Also making a couple of instructional videos, since that is usually better than reading a long boring guide.

If you have any problems, questions or would just like to chat, please contact me on lukasz.migas@manchester.ac.uk.

Thanks,

Lukasz Migas

Publication: Migas et al. ORIGAMI: A software suite for activated ion mobility mass spectrometry (aIM-MS) applied to multimeric protein assemblies

ORIGAMI-MS

An initial release of ORIGAMI^MS.

ORIGAMI^MS is part of ORIGAMI software suite that aims to increase the efficiency of acquisition and analysis of activated Ion Mobility-Mass Spectrometry (aIM-MS) datasets. ORIGAMI^MS is utilising the Waters Research Enabled Software (WREnS) to perform a sequential increase of the collision voltage in the cone or trap region of the Waters Synapt G2/G2S and G2Si instrument on small molecules, proteins and anything that flies 😄.

This version of ORIGAMI^MS enables acquisition using the Graphical User Interface (GUI) or as executed from command line.