PLGS Threshold Inspector Files

PLGS Threshold Inspector
v2.4
1. Finally changed tooltip on the export grid as new user defined Threshold button.

For those of you using it through the command line these are the other changes that might be of interest to you. 
If you don't use the command line interface then there really isn't any need to update.
2. Added three new command line switches so that different threshold grids can be specfied through the command line.
See PLGS Threshold Inspector Command Line Interface for v2.4.pdf for a longer explanation.
They are:
	MissingThresholdId
	NotRunThresholds
	OverrideThresholds
3. Added a list that you can copy to the clipboard of the allowable commandline arguments. It's on the Options page.

v2.3
Fixed the longstanding bug with the progress bars. The Peptide and iaDBs bars now update as intended ie they update.
Added two new features:
1. Create pkl and mgf (MassLynx peak list and Mascot generic file) from the Peptide3D output.
2. Save the protein search results
You enable them both through the options dialog. Create pkl and mgf is on by default and save protein search is off.

1. Means that your MSe data can now be treated as though it were DDA. If you want to use it to search for proteins then you have to sort that out yourself. The Matrix Science web site would be a good place to start.
Pkl files contain an entry for every detected low energy peak regardless of the number of matching high energy peaks.
Mgf files only contain entries for low energy peaks that have matching high energy peaks.
These files are saved into the raw folder and prefixed with the time window and LE/HE parameters they were created with.
There are one of each file for every set of thresholds you process.

2. Means that you can look at the resulting proteins from your search. The output from iaDBS contains the final proteins, final peptides and final fragments.
It's up to you what you do with these. There is no visualisation, just the results in csv files.
These files are saved into the raw folder and prefixed with the time window and LE/HE parameters they were created with.
There are one of each file for every set of thresholds you process; three for each set of thresholds.

v2.2
Fixed bug that deleted the User Defined Values saved file when the application closed.
Added new button on the interface to export the current threhold grid as the user defined values.

v2.1
Add command line interface. See PLGS Threshold Inspector Command Line Interface.pdf in the installation folder for more explanation.
Changed the 'few' thresholds to a more sensible range.

v2.0 
Build 8
Release. Version expiry removed.

Build 7
Added 64 bit operation to support large Apex bin files
Added second Y axis to Good Ions graph

Build 6
Changed error handling for the condition when ApexFilter runs out of memory because the input Apex.bin file has too many peaks to handle.
On this error the processing stops. Red cross indicates error processing that step.

Build 5
Added indicator icon next to filename which describes if it is an MSe file.
Fixed crash on selection of blank grid when no file selected

Build 4
Added icons for grid shortcuts
Added graphs plotting LE, HE, LE vs HE as heat map and ApexGood Ions
Added user defined list of threshold values which are used if a file has never been processed.

Build 3
Added copy grid to clipboard. So I'll leave it up to you folks to tell me what kind of graphs to plot.

Build 2
Exposed the independent lockmass values for charge state 1 and 2
Added buttons for select all and deselect all


Build 1
Change of approach
Run Apex once with the lowest selected thresholds.
Filter from this single file.
Massive time saving as Apex is run only once.
Nothing else has changed (yet).

v1.0
Realease as v0.3.2, but without expiry.

v0.3.2
Changed database file browser filter to *.fas* so .fasta files can be selected.

v0.3
Deleted the filename quality check (the tick/cross by the filename). This has been calling all sorts of problems and is probably something close to the root cause of the non-starting of processing when you press play.

Added a catch around Peptide and IA csv file readers to force non-numeric values to be 0. It turns out that IA can occasionally return a blank field instead of a numeric one. Who would have guessed that?