Update 2018 July 03
Previously you had to select both ResCalc and PeakID if you wanted the Chromatogram masses to be the query. If you didn't then the list stopped after the first entry.
That is now fixed. You no longer have to specify ResCalc and PeakID. You only have to specify which one you want.
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Should have put this out back in April when v1.14 dropped.
Anyway, too late to worry about that now. Here's the readme.
Version 1.14
This is the release that precisely no one whatsoever asked for!
It's packed with new features that are unlikely to make any difference to anyone.
Feature changes:
1. Chromatogram Combine Range now supports both "BPI" and "TIC" as a Mass value.
In the mass column press b or t to fill with either BPI or TIC.
Typing the mass value in still works just as it always did.
A mass of "BPI" or "TIC" is reflected all the way through into the xml reports.
A mass of "BPI" or "TIC" is reflected as numeric values of -2 and -3 respectively in the text file outputs.
In the setup the values of mass tolerance for BPI and TIC are populated, but ignored in the query.
Although BPI and TIC will be pushed into the Resolution and Peak ID query if you ask it to the values are meaningless and the line in the report will be a null result. (Just think about how you would go about determining the resolution of the peak at mass BPI in a spectrum.)
2. Chromatogram Combine Range can now be forced across all functions.
Previously a query was applied only to its nominated function.
By checking the (new) column "4All" on the end of the row the detected scan range is forced onto all functions of the acquisition.
"4All" means "Apply this range to all functions" - which is too long for a column title.
This applies to all functions regardless of the starting function.
If you have 3 functions and detect on Fn1 it is applied to 2 and 3 as well.
If you have the same 3 functions and detect on Fn3 it is applied on 1 and 2 as well.
This is supported across all rows independently. You are not limited to having just one row in the query if this is enabled, although using it with multiple rows is very overwhelming. And you can mix up the enable state across rows.
If you had the 4 function acquisition mentioned in the example use case below and you had a three row query (TIC, BPI and a numerical mass) and using the MassLynx Peak Detect option you detected two peaks in each query the overall result would be 24 ranges ( 3q, 2pk, 4 Fn). Note SpecProc peak detect only ever returns one peak (the highest).
Here is a use case that you might or might not find illuminating:
You have a 4 function acquisition where each of the functions has an increasing cone voltage or maybe collision energy, either way something that means that the spectral content is a bit different in each function.
The TIC contains peaks where your thing of interest appears. These might be lovely smooth LC or GC peaks or rough probe insertion peaks.
You want to get at the scans that span the peak in all of the functions, not just the first (or second etc.). This is because that range of scans is the information for that peak at the conditions defined by your function conditions.
But what you really want is to make sure you have exactly the same range on all functions; this is important to you.
So if you set up a method where there was (for example) a BPI detect on each of the 4 functions there is no guarantee that this would return exactly the same range on each of the detects.
This is especially true if there are multiple peaks in the acquisition. In addition you would have to maintain the method for every variation of acquisition that you came across.
For example if your acquisition had three functions or five then you would need new methods.
What you really want to do is define a peak detect to the effect of "Go find a peak in Fn1 and then whatever range you find use it across all the functions."
And now you can.
Provided that you set a type of peak detect and enable the auxiliary files then you would generate text files of the peak lists which you could then combine or send to a library etc.
That part is up to you. There might be an app out there already that can help you with this step.
Top tip: If you have quad data increase the minimum width value in the Centre options. This will eliminate lots of the grass in the spectrum. It's more efficient than smoothing.
3. The web pages views are now portable.
This might sound a bit odd, but up to now behind the scenes in the web page there was a static link to "C:\MassLynx\SpectrumTools\resouces".
This meant that to display the pages correctly you had to have these resources in exactly this location; which is fine if you had SpecProc installed, but if you moved and saved the files on another PC then you could get into all sorts of display problems, none of which were your fault.
The new default option in the Editor is to use "Local resources for web page formatting". This makes a copy of the resources in the same folder as the results.
This does indeed increase the size of the folder, but also means that provided you copy the whole folder the results display correctly wherever you copy it to.
Old methods remain at static location.
Bug fixes:
1. The installer now deletes SpeProcEditorRecentFileList.xml.
Having a previous version of this file caused an error on load message in the Editor.
This file must be deleted or uninstalled when you change versions.
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Update 2018 July 03
Previously you had to select both ResCalc and PeakID if you wanted the Chromatogram masses to be the query. If you didn't then the list stopped after the first entry.
That is now fixed. You no longer have to specify ResCalc and PeakID. You only have to specify which one you want.
Should have put this out back in April when v1.14 dropped.
Anyway, too late to worry about that now. Here's the readme.
Version 1.14
This is the release that precisely no one whatsoever asked for!
It's packed with new features that are unlikely to make any difference to anyone.
Feature changes:
1. Chromatogram Combine Range now supports both "BPI" and "TIC" as a Mass value.
In the mass column press b or t to fill with either BPI or TIC.
Typing the mass value in still works just as it always did.
A mass of "BPI" or "TIC" is reflected all the way through into the xml reports.
A mass of "BPI" or "TIC" is reflected as numeric values of -2 and -3 respectively in the text file outputs.
In the setup the values of mass tolerance for BPI and TIC are populated, but ignored in the query.
Although BPI and TIC will be pushed into the Resolution and Peak ID query if you ask it to the values are meaningless and the line in the report will be a null result. (Just think about how you would go about determining the resolution of the peak at mass BPI in a spectrum.)
2. Chromatogram Combine Range can now be forced across all functions.
Previously a query was applied only to its nominated function.
By checking the (new) column "4All" on the end of the row the detected scan range is forced onto all functions of the acquisition.
"4All" means "Apply this range to all functions" - which is too long for a column title.
This applies to all functions regardless of the starting function.
If you have 3 functions and detect on Fn1 it is applied to 2 and 3 as well.
If you have the same 3 functions and detect on Fn3 it is applied on 1 and 2 as well.
This is supported across all rows independently. You are not limited to having just one row in the query if this is enabled, although using it with multiple rows is very overwhelming. And you can mix up the enable state across rows.
If you had the 4 function acquisition mentioned in the example use case below and you had a three row query (TIC, BPI and a numerical mass) and using the MassLynx Peak Detect option you detected two peaks in each query the overall result would be 24 ranges ( 3q, 2pk, 4 Fn). Note SpecProc peak detect only ever returns one peak (the highest).
Here is a use case that you might or might not find illuminating:
You have a 4 function acquisition where each of the functions has an increasing cone voltage or maybe collision energy, either way something that means that the spectral content is a bit different in each function.
The TIC contains peaks where your thing of interest appears. These might be lovely smooth LC or GC peaks or rough probe insertion peaks.
You want to get at the scans that span the peak in all of the functions, not just the first (or second etc.). This is because that range of scans is the information for that peak at the conditions defined by your function conditions.
But what you really want is to make sure you have exactly the same range on all functions; this is important to you.
So if you set up a method where there was (for example) a BPI detect on each of the 4 functions there is no guarantee that this would return exactly the same range on each of the detects.
This is especially true if there are multiple peaks in the acquisition. In addition you would have to maintain the method for every variation of acquisition that you came across.
For example if your acquisition had three functions or five then you would need new methods.
What you really want to do is define a peak detect to the effect of "Go find a peak in Fn1 and then whatever range you find use it across all the functions."
And now you can.
Provided that you set a type of peak detect and enable the auxiliary files then you would generate text files of the peak lists which you could then combine or send to a library etc.
That part is up to you. There might be an app out there already that can help you with this step.
Top tip: If you have quad data increase the minimum width value in the Centre options. This will eliminate lots of the grass in the spectrum. It's more efficient than smoothing.
3. The web pages views are now portable.
This might sound a bit odd, but up to now behind the scenes in the web page there was a static link to "C:\MassLynx\SpectrumTools\resouces".
This meant that to display the pages correctly you had to have these resources in exactly this location; which is fine if you had SpecProc installed, but if you moved and saved the files on another PC then you could get into all sorts of display problems, none of which were your fault.
The new default option in the Editor is to use "Local resources for web page formatting". This makes a copy of the resources in the same folder as the results.
This does indeed increase the size of the folder, but also means that provided you copy the whole folder the results display correctly wherever you copy it to.
Old methods remain at static location.
Bug fixes:
1. The installer now deletes SpeProcEditorRecentFileList.xml.
Having a previous version of this file caused an error on load message in the Editor.
This file must be deleted or uninstalled when you change versions.