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 TIC and BPI 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 function 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.

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Update 2018 July 12

SpecProc 1.3

This is the update for the latest versions of MassLynx that run on Windows 10 (and also on Windows 7). It is needed as one of the internal MassLynx file formats has changed. If you have this type of MassLynx then SpecProc won't open, but the editor does. That is the clue.

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Update 2018 July 03

For SpecProc 1.12

Fixed bug where both ResCalc and PeakID had to be selected for the correct list of Chromatogram masses to be processed.

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Version 1.12_B (app 1.12.4)

Fixed bug where queries were processing in the wrong sequence if a mass had no matching chromatogram peaks.

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Version 1.12

As v1.11 except query mass list behaviour modified. If 'Use chromatogram mass for query' is selected it now only performs Res and/or Peak ID on the extracted mass, not all of the masses in the chro_extract list. This gives you the diagonal line of results without any need to apply rejection filters in the Res and Peak ID queries. The other queries are unaffected and always process everything for every combine range.

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Version 1.11

As v1.10 Fixed bug where Apex chro peak detect didn't produce any results. Fixed bug where MassLynx chro peak detect on SIR data did not produce any results. Added quad peak width as a resolution choice. Added the Name field to chro peak detect option. Added Use field to chro peak detect option. If set the query is used, if un-set the query is skipped. Can now sort the columns of the chro peak detect option. Added choice of mDa or ppm to the search windows in the Spectrum query. You can now move masses in the Res and Peak ID mass lists up and down. Added Append or Overwrite as a choice after selecting Res/Peak ID masses from a file. You can now click on the chro query column to toggle ppm/mDa, Use, Use Min Int and Use RT Limit Added the ability to move masses up and down the list in Res and Peak ID query. Resolution asymmetry is now reported against the centroid of the top 50% of the peak height. The text files also include the asymmetry against the peak top. The default asymmetry detect height has been reduced from 0.02 (2%) to 0.01 (1%)

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Version 1.10

As v1.9 Editor files from previous versions might not open correctly in this version of method editor.

Added support for using SIR/MRM channels to define the extracted mass chromatogram. If channels are used no processing is performed regardless of the method settings; channels mean SIR/MRM, so no spectral data. Get the chromatogram peak detection results from the _chroinfo.txt file in the data or results folder.

Revised the Specproc chromatogram peak detect method to cope more accuratly with partially resolved peaks. The change in algorithm makes the peak detection less sensitive to edge effects. It also has the effect of moving the centroid towards the unresolved edge. Empirically this is about 4%. If this information is used for Mobility Test specs then the calculated resolution will be lower by the same % that the peak has shifted compared with previous methods.

Build 6 Added stats reporting to chromatogram detect methods. If using SpecProc detect then parameters are averaged across batch (as there is only one peak per query row). If using MassLynx detect then parameters are averaged across query row (as there can be more than one peak per query row). Revised the summary reports: Moved the display control buttons Added test for correct configuration of IE so that scripting is enabled. Added conditional buttons for when chro detect results are used. Added buttons to show/hide chro stats, chro results. The chro query is always displayed. Added a new chroinfo report. Added link in individual Spe query reports to the new chroinfo report (when its applicable).

Editor build 3 Parameters that are multiplied by the TDC/ADC ratio are now shown in red if TDC/ADC conversion is used. This highlights that these parameters are modified. *Don't forget that if you just want to use the numbers as they are then switch off this option. Chro peak query intensity labled renamed to 'Height'. This now matches bith the report title and MassLynx nomenclature. Chro peak detect Height now correctly handles large numbers.

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RELEASE 1.9

Build 1 As builds 37 and 26. Added space between value and % on Quantify average text outputs. Appears in merged xml. Fixed bug that the quantify average pass/fail was incorrectly determined. It now compares it to the state in the query, rather than always greater than. Changed the way that the "Open the last SpecProc Summary page" shortcut works. It no longer makes a new set of files. It now just opens the last list of merged files.

Editor build 2. The Do-TDC/ADC conversion flag is now read from the olp file (as well as still writing it out to the olp file). Previously the flag was at the editor level rather than the olp level. So you could change the status without realising. Fixed bug with display of Chromatogram Peak Detect Method. Radio buttons were incorrectly grouped due to an error in XP manifest translation.

App build 3 Changed peak turning rule on res detection. Peak turns if two consecutive data points are in the opposite direction to the current point.So if there is a one bin glitch it will be rejected.

Editor build 5 Fixed bug where the last saved file, rather than last opened file, was opened on app start. The window title was displayed with last opened, so these things did not match. The app now opens the last opened file and displays the last opened file name when the app starts.

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Version 1.8

Added TDC/ADC conversion factor support.

Added retention time limit on Chro peak detection.

Added a choice of chromatographic peak detection; SpecProc single peak find or use MassLynx

Fixed bug that if Chro peak detect was specified in mDa and the olp file was re-opened then the units were incorrectly read and turned into ppm.

At the end of the sample list batch the following file will be run, provided that the file is there: C:\Masslynx\SpecProc_NextApp.bat You can change the app by creating the resgistry key: HKEY_CURRENT_USER\Software\VB and VBA Program Settings\SpecProc\Parameters\NextApp

e.g. To launch paint (?) after SpecProc finishes... HKEY_CURRENT_USER\Software\VB and VBA Program Settings\SpecProc\Parameters\NextApp\C:\WINDOWS\system32\mspaint.exe

The files ...\AppPath\SpecProcLastResultsLocation.txt and ...\AppPath\SpecProcLastResultsLocation.xml are now created. These contain the location of the last Chroinfo file created. The information is the same in the two files.

Fixed bug that if the meant that everything to the left of the colon was removed if the text was 1:46. This was being reported as :46

Added more info to ChroInfo.txt header. Olp filename, sample text, bottle number/Sample well and instrument number.

The Masslynx.ini param AutoParams is always set TRUE, unless the olp override is on, then it is set to whatever you ask for.

Fixed bug with chropeak detect. Was inaccurate when retention time limit was used.

Fixed bug that processing dropped out rather than reported a message when sorting by intensity.

Fixed intermittent bug whereby using Masslynx integrate no peaks were detected.

Added Asymmetry measurements to resolution calculation.

In the summary report added button to toggle visibility of the statistics tables.

Fixed bug which had incorrect logic for the overall pass of Peak ID when using Signal to Noise query.

Fixed bug that incorrectly calculated the averages. Previously the invalid rows were included in the sum.

Added XP styling to Editor and Application.

Added multiple column layout to the summary results page. This is selected by the user. Note that the Averages only describe the primary parameter. Mass Difference does not have a multicolumn view.

Fixed bug that user masses were tuncated to 7 significant figures when reloading a method. They were always saved ok and read by the application ok, it was just the reloading. Masses are no longer truncated. So 1570.6774 no longer comes back as 1570.677

Fixed bug in Peak Id style sheet that did not disaplay S2N values if Report Intensity Pass/Fail was not selected.

Fixed bug that reference file masses were incorrectly trunkated. The wrong data type was used so masses above 1000 were limited to 3 decimal places. They are now correctly trunctaed to 4 dp.

Build 30. Adds the sample text to the end of each line in the text file.

Build 31. Changed spectral asymetry calc so that it is now the ratio of 10% widths either side of the centroid.

Build 32. Fixed bug so that a Quad Daughter scan (which doesn't stamp a set mass) is correctly handled. This means that you can now select combine all chromatogram for this data type.

Build 33. Added chro asymetry at the user specified %height to _chroinfo.txt. This is using interpolation of %height.

Build 37 and Editor 26. Added Quantify pass/fail criteria.

RELEASE 1.9 Build 1 As builds 37 and 26. Added space between value and % on Quantify average text outputs. Appears in merged xml. Fixed bug that the quantify average pass/fail was incorrectly determined. It now compares it to the state in the query, rather than always greater than. Changed the way that the "Open the last SpecProc Summary page" shortcut works. It no longer makes a new set of files. It now just opens the last list of merged files.

Editor build 2. The Do-TDC/ADC conversion flag is now read from the olp file (as well as still writing it out to the olp file). Previously the flag was at the editor level rather than the olp level. So you could change the status without realising. Fixed bug with display of Chromatogram Peak Detect Method. Radio buttons were incorrectly grouped due to an error in XP manifest translation.

App build 3 Changed peak turning rule on res detection. Peak turns if two consecutive data points are in the opposite direction to the current point.So if there is a one bin glitch it will be rejected.

Editor build 5 Fixed bug where the last saved file, rather than last opened file, was opened on app start. The window title was displayed with last opened, so these things did not match. The app now opens the last opened file and displays the last opened file name when the app starts.