MSQuant is a tool for quantitative proteomics/mass spectrometry and processes spectra and LC runs to find quantitative information about proteins and peptides. Though automated it also allows manual inspection and change.
MSQuant’s main purpose is to make quantitation of proteins and peptides possible in the area of mass spectrometry/proteomics (science/analytical chemistry/molecular biology). E.g. an experiment where one heavy isotope-labelled sample from treated cells is compared to unlabelled, untreated cells to give quantitative answers about cellular processees. The input to MSQuant is a search result file (HTML) from the Mascot search engine (from Matrix Science) and one or more raw spectrum files.
MSQuant is written in Microsoft’s .NET and thus can only run on Windows computers that have the .NET runtime installed. The runtime is installed by default in later versions of Windows.
This program was directly referenced in the paper "A novel proteomic screen for peptide-protein interactions" (PDF) by Waltraud X. Schulze and Matthias Mann. 2003. Journal of Biological Chemistry (JBC). Abstract.
It was also the basis for the Nature paper "Proteomic characterization of the human centrosome by protein correlation profiling" (PDF) by Jens S. Andersen, Christopher J. Wilkinson, Thibault Mayor, Peter Mortensen, Erich A. Nigg, Matthias Mann. 2003. Abstract. Full text. On 2004-02-16 this paper was number 4 on Nature’s top 10 most downloaded papers.
SILAC is originally described in "Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics." (full text) by Ong SE, Blagoev B, Kratchmarova I, Kristensen DB, Steen H, Pandey A, Mann M. 2002. Abstract 1. Abstract 2.
SILAC is described in greater detail in "Properties of 13C-substituted arginine in stable isotope labeling by amino acids in cell culture (SILAC)." (full text NOT available online) by Ong SE, Kratchmarova I, Mann M. 2003. Abstract.
Triple encoding for SILAC is described in "Temporal analysis of phosphotyrosine-dependent signaling networks by quantitative proteomics." (full text as PDF file) by Blagoev B, Ong SE, Kratchmarova I, Mann M. 2004. Local copy. Abstract.
MS3 scoring is described in "Improved peptide identification in proteomics by two consecutive stages of mass spectrometric fragmentation" by Jesper V. Olsen and Matthias Mann. 2004. As PDF file. Abstract.
MSQuant is written in C# for .NET and in Visual Basic for .NET (VB.NET). It has an export facility to transfer information to databases that is supported by the .NET framework. For access to information in spectrum files it depends on vendor supplied COM components/libraries from (currently) three commercial packages, Sciex’s Analyst, Finnigan’s XCalibur and Micromass’ MassLynx.
2008-05-30.
Fourth official release
of MSQuant!!!. Version 1.4.3.
Added since b4: menu commands added to the Protein List window to open the containing folder for the Mascot Result file and the raw file.
Tips:
2008-05-29.
Public
beta testing programme for MSQuant v. 1.4.3. Beta version 4:
1.4.3b4 ( 4.8 MB).
16 hours remain of the beta testing programme.
Please report bugs as soon as possible.
Additions, changes and bug fixes since v. 1.4.3b3 (2008-05-27):
Export functions work again and it can now be made to work on all systems - a very long standing bug that mysteryously made it not work on some systems is history... And it has been extended: 1. Direct export to Open Office's spreadsheet program, Calc. 2. Any application can be selected to open the output from the export functions. 3. If the export goes to a file then optionally it can be opened after being saved to disk using Windows's settings (Windows Explorer, menu Functions/Folder settings/ tab File Types/ Change), e.g. .TXT files opens in Excel (instead of Notepad or UltraEdit). MSQuant stores common install locations for Calc and Excel. If you have installed the applications in some other location then it can be made to work if you add the installation folder to the PATH (same way as for Analyst/QSTAR, described on this page).
2008-05-27. For developers:
7-Zip package for MSQuant v. 1.4.3b3
(0.7 MB) with source code and other files.
Google indexable version.
Project MSQ1lib is now a C# project. Most C# source
files have been moved from the FastSerialisation
project to the MSQ1lib project.
2008-05-27.
Public
beta testing programme for MSQuant v. 1.4.3:
1.4.3b3 ( 5.0 MB).
The beta testing programme will last 72
hours, starting from 2008-05-27T13:00:00Z.
Please report bugs as soon as possible.
Known bug: the Export functions are broken, the corresponding Save functions must be used instead. An attempt will be made to fix this problem in the beta testing period.
Additions, changes and bug fixes since v. 1.4.3a74 (2008-03-07):Relocation of full file paths in MB3. MB3 files can now be moved to a different computer that has different drives and paths. This means you can also move Mascot result files and raw files to a different location without the fear that MB3 files will be useless.
Terminal modifications (e.g. O18 or Dimethyl N-term) are now supported in quantitation modes. Previously it only worked for computing correct fragment masses in the Protein Validation window. The correct masses are now computed and the majority of the peptides are no longer rejected during parsing.
Ion series has now been generalised instead of being fixed to b, y and y++. Any ion series can now easily be specified and the set to use can depend on some rules, e.g. on a modification, like phosphorylation. In this version things are hardcoded; if modification ID is 5048 ("Phospho (ST)" in standard CEBI version of settings file "new_MSQ_quantitationModes.xml") 8 extra ion series are used - y-98, y++-98, y- 196, y++-196, b-98, b++-98, b-196 and b++-196.
The dialog for save/export has been extended to include an option for spectrum line (LC point) information. This correspond to some old menu commands in the Quantitation windows, but you can now export this information for any protein subset from the Protein List window.
All OK buttons and Cancel buttons in all dialogs now have the standard keyboard shortcuts: Enter for OK and Esc for Cancel.
Now tolerant of old MB3 files with PTM scores of -Infinity. The Export/Save now succeeds. There are ASSERTs, but they have been greatly decreased in number.
All buttons in all dialogs now have an Alt keyboard shortcut. E.g. Alt+O for the OK button.
Protein Validation window: option to display unmatched ions or not. As a nice side-effect PTM (and MS3?) scoring is much faster when unmatched ions are not displayed.
Recalibration reality check. Dialog for entering e.g. minimum number of peptides for recalibration. This new feature also replaces the hardcoded limit of 4 for the minimum number of data points for recalibration. Started by a new button in the Options dialog: "Reality check..." Limitation: the settings are not (yet) remembered across program restarts.
Selection now works for the peptides in the Quantitation windows. E.g. you can now quantitate any subset of a protein's peptides. This replaces older menus command and buttons.
Matched ions in the Protein Validation window are now separated vertically from the unmatched ions.
All dialogs are now much closer to follow the standard: no resize handle, borders look like standard dialog borders, etc.
The Protein Validation window is taller now. This may or may not cause problems for some notebooks...
In Tools/Options dialog: "Preselected peptides" is now "PSPs".
the horisontal aligment for numbers in lists in the Protein List window, the Protein Validation window and the Quantitation window was changed from left alignment to right alignment.
In the Quantitation window: now always scrolls the spectrum list in the upper right so the spectrum line for the maximum LC point is visible (the spectrum data points are displayed in the lower left). This bug was probably very, very old.
All non-quantified peptides are no longer quantified on reopening the Quantitation window if one or more peptides have already been quantified. This resulted in unexpected long delay on opening the Quantitation window, perhaps even the belief that MSQuant had frozen.
Removed cause of this exception that could happen on exporting PTM scored peptides: "Could not export the selected XXX proteins". This problem exposed a problem deep down in the bowel of MSQuant. The implementation of "n over k" used in the computation of the PTM score (and MS3 score) could not handle n greater than about 170 and the result was a PTM score of Infinity or NaN ("not a number"); and later problems during export/save of PTM scored peptides.
ASSERT when displaying a peptide in Protein Validation window that pointed to the last fragment spectrum in a raw file. ASSERT message: "nextFragmentspectrum2() returned negative value - no fragment spectra past spectrum 10935".
the file that information is exported to is now closed by MSQuant when it is ready. Thus this file can now be deleted or renamed without having to resort to close MSQuant...
A problem with gi accession numbers and saving spectrum data points has been fixed. (The "|" from the gi accession numbers that was part of the proposed file name is not valid in a file name in M$ Windows)
Now gracefully handles if the number of (predicted) PTM combinations is greater than 2147483647.
Removed: harmless, but irritating and misleading ASSERT for some long peptides when displaying them in the Protein Validation window. (Limit is now 1200 instead of 500. For a sample peptide the count was about 800)
Is now compatible with raw2msm. If the start retention time output by raw2msm was 0.0 minutes then an ASSERT would occur.
2008-03-07.
Development (alfa) version of MSQuant:
1.4.3a74 (12.2 MB).
(Is in the 7-Zip format, not ZIP.
The 7-Zip software is
open source and an
installer is available).
This is primarily a bug-fix release.
LTQ-Orbitrap aware recalibration. Menu Tools/Options/ Recalibration of preselected peptides (precursor mass)/ Domain/Frequency, 1/f^0.5 (Orbitrap).
New kind of plot added to recalibration Visualisation window: retention time vs. mass error. This makes it easier to spot if there was a mass drift during a run - set the peptide filter to narrow mass range to exclude any mass dependent mass error.
New unit in the Recalibration Visualisation window: ppb - part per billion. This makes it easier to read off values in the binning view as values are larger than one for most bins.
The Quantitation window finally got a distinct icon... And the Recalibration Visualisation window got one as well.
Proteins are now included in the protein list even if all peptides are low scoring (not in A,B,C). This corresponds to a different setting of a checkbox that was once in the Options dialog: "Do not show proteins without peptides in A, B or C". The protein score for those proteins is zero.
Now uses theoretical MCR instead of measured MCR in the Recalibration Visualisation window. This prevents unexpected sloped set of points for very high zoom states.
Now works again if there are no datapoints in the display mass range for the LC point to be quantified. The symptom was: "Arithmetic operation resulted in an overflow" This bug was introduced on 2008-01-31 with the theoretical isotopes markers. Workaround for older versions: exclude the peptide in question from the quantitation window somehow, e.g. clicking it off in the Protein Validation window (and saving to MB3 anew, etc if to be used from the BAT script).
Two problems related to peptide filter option "Highest scoring uniquely modidied" for the preselected peptides during parsing: a. The protein score is now correct. It would include peptide scores for the peptides excluded by the option. b. The peptide count in A,B,C (e.g. displayed in the Protein Validantion window and in the export) is now correct. It would include peptides that were excluded by the option.
Problem with the colours during zooming in the Recalibration Window. It was nearly impossible to see the zoom bounding box.
Combined files, menu Tools/Correlation Settings/Insertion of new peptides/Insert peptides only in range: the restriction on the retention time range for insertion of new peptides now works again. It was completely broken on 2007-01-08 (unless the range was specified in hours instead of minutes ...).
If the recalibration for a raw file can not be computed due to no peptides for recalibration (depends on peptide filter) then it is now effectively turned off; slope is set to 1.0 and offset to 0.0. The symptom was a very large number of message boxes with this text: "Calibration constants not found for key 811".
ASSERT during quantitation if a peptide was identified from a spectrum within 15 seconds of the end of the raw file (for the default -60s/+90s setting). This problem was thought to have been fixed on 2006-08-28. But it turned out only to be true if more than 15 seconds from the end of the file... Workaround for older versions: exclude the peptide in question from the quantitation window somehow, e.g. clicking it off in the Protein Validation window (and saving to MB3 anew, etc if to be used from the BAT script).
Combined files: now works if a predicted retention time happens to hit a region at the end of a spectrum file with only MS spectra... Symptom was: "PIL ASSERT. Spectrum number, 18981, is outside the range for the raw file, [1; 18980]". Note: these peptides are not inserted.
Quantitation window: menu File/"Export peptide with spectrum list" no longer causes an exception if the current peptide has not been quantified.
Recalibration Visualisation window. An exception is no longer thrown if the peptide filter is set such that all peptide MCRs are equal, e.g. only one peptide comes through the filter. The rather misleading error message was: "Could not read values dialog in dialog. Some numeric fields may hold letters, etc. Error: System.IndexOutOfRangeException: Index was outside the bounds of the array.".
2008-02-26. DTASuperCharge, version 1.19 (11.4 MB) - an application for converting one or more Finnigan .RAW files to Mascot search input files in a format suitable for use with MSQuant. Bug fixed: a trailing space is now output after the rawFile field (in the TITLE line). This bug made it more difficult to specify a robust parsing rule for MSQuant..
2008-02-11. For developers:
7-Zip package for MSQuant v. 1.4.3a59
(0.7 MB) with source code and other files.
Google indexable version (no longer available).
File PILinOut.vb was moved from
MSQuant/msquant/src/main/spcommon/ to
MSQall/MSQlib1/src/Utility/.
New C# source files have been put into the FastSerialisation
project/folder for the time being.
2008-02-11.
Development (alfa) version of MSQuant:
1.4.3a59 (4.3 MB).
(Is in the 7-Zip format, not ZIP.
The 7-Zip software is
open source and an
installer is available).
There is a lot of changes that will give different
results than previous versions, e.g. PTM scoring and
use of isotopes in quantitation.
The TITLElineParseDefinitions block in the settings
file new_MiscOptions.xml is now read by MSQuant and
the way information is extracted (from what is in
TITLE lines in the MGF file) is now thus
user-defined. Adding a new definition it should be possible to
directly parse files originating from other MGF file generators.
The main window (blue) can now be resized!!!
The Enter key can now be used to open spectra from quantitation spectrum list (in addition to double-clicking).
LTQ-FT aware recalibration (menu Options/Recalibration of preselected peptides/Domain/Frequency (LTQ-FT)). This will assign proper weights to the datapoints for recalibration; high MCR will not affect the recalibration result more than necessary.
Post-parse recalibration is now possible. Note: if you use a subset of the proteins to find the recalibration then the recalibration correction is still applied to ***all*** proteins. That is the reason for the exact same number of peptides in the Recalibration Visualisation window. If you want to review only the peptides that were used for recalibration you can use an existing function (menu Automation/Recalibration Visualisation. It works on the selection). Set the peptide filter in the Recalibration Visualisation window to the same as the filter in the options dialog. This is not an exact match as a peptide may be excluded if there are more than 300 available or if rejected in outlier elimination - but it is still useful.
New menu item for Protein List window: Report Raw Files Information. This makes it easier to evaluate the recalibration result for each raw file. E.g. the changes in ppm for low and high MCR are reported. Information about each file include: a. File without path. b. Internal code number: 1789, 809- c. Recalibration constants (for this raw file). d. After calibration value for the highest and lowest MCR. And corresponding absolute and relative differences to the two MCR values. e. Full file path.
The raw file ID (1789, 809-) has been added to the export.
Raw file filter to the peptide filter dialog. This is another tool for evaluation of the recalibration result for each raw file.
More default parsing rules to handle multiple raw files: 1. for QS 1.1 or later output 2. for newer versions of DTASuperCharge (assuming using a simple merge of MGF files - e.g. manual) that has a bug with missing trailing space. 3. for the newest versions of DTASuperCharge, 1.19, with the trailing space bug fixed. Thus for combined QSTAR files the output from Mascot.dll can be used directly! No scripts or other software is required. Warning: has only received minimal testing. To see the new rules you can rename settings file "new_MiscOptions.xml" and restart MSQuant. This will reset the very important quantitation window settings. Thus you should replace the blocks "quantitationSettings" and "PTMscoreSettings" in the new file with the content from the old file.
The recalibration trendline is now plotted (5 artificial points are added on this line to make it easier to spot non-linear lines). This line will only be linear if corresponding to the recalibration. E.g. it is not linear if unit is ppm and recalibration was done in the mass domain or if done in the frequency domain and plotted in Th.
Display of recalibrated peptides is now optional so that it does not have to be displayed every time. HOWTO: menu Tools/Options/button/"End of parse action..."
The theoretical isotope cluster heights are now indicated on the MS spectrum in the Quantitation window. It is the actual values for the current peptide, not just averagine. Current limitations: SILAC purity (e.g. 98.5%) is not taken into consideration and thus the values indicated for the non-wild isotope clusters are higher than they should be. The pre-peak height is not predicted either (but the program has been prepared for it). It does not work with zooming either.
Two new kinds of plots have been added to the lower right in the Quantitation window: a. LC profile visualisation using the same kind of plotting as for recalibration visualisation: the plot can be zoomed, panned, reset back to original scale, pop-up information for each data point, etc. It is read-only, but will hopefully in the future it will have the interactive features of the classic LC profile plot. b. Spectrum-to-spectrum SILAC ratios as a function of retention time. Makes it easy to spot trends caused by e.g. non-coeluting SILAC peptides.
File extension in opper-case in the Mascot result file is now accepted. E.g. a peptide with this information can now be succesfully parsed: rawFile: 20080117JEA_SILAC2_1_06.RAW
PTM-scoring is now different : n for PTM score was too high (and thus PTM score too low) due to a mass range set to the theoretical fragments mass range and not the mass range for the (observed) data. Example: For protein 1 in some data set: peptide GVMNAVNNVNNVIAAAFVK now get a PTM score of 80.1 instead of 72.8. The Mascot score is 88.0.
Now uses multiple isotopes for quantitation. In this version it includes the first isotope in the quantitation result. Future versions will be more sophisticated, including more isotopes depending on constraints like collision with the next SILAC isotope cluster group. The peak(s) used for quantitation are indicated in the MS spectrum in the Quantitation window. There will only be one if there is no signal for mono isotopic peak. This prevents spurious results if the isotope mass interval happens to pick up some (unrelated) data points.
Recalibration now has outlier-elimination. The algorithm used for this purpose is thought to be very robust and results are as expected sofar, but it remains to be critically tested (e.g. C13 masses with the previous implemented C13 correction turned off).
Recalibration is now done independently for each raw file (for merged files).
There is now a limit to the number of PTM combinations. This has been tested on an example that took 2 minutes to complete and on one that would have taken nearly 4 days (VSQTPIAAGTGPNFSLSDLESSSYYSMSPGAMRRSLPSTSSTSSTK, 2oxM 3pST 1pY 6ipSTY 1hex). The limit for the number of combinations has a default value of 1000. It is specified through a field in settings file "new_MiscOptions.xml": maxCombinations in PTMscoreSettings. Sample:
<PTMscoreSettings>
<PTMminimumScore>14.000</PTMminimumScore>
<maxDisplayedPTMcombinations>25</maxDisplayedPTMcombinations>
<minimumPTMdeltaScore>0.1</minimumPTMdeltaScore>
<maxCombinations>18000</maxCombinations>
</PTMscoreSettings>
It is now much easier to zoom to the first and the last datapoint in a spectrum...
Recalibration itself is now somewhat more efficient with regard to memory and speed. It no longer go through all proteins and peptides. It now stops when the maximum of 300 peptides for recalibration has been reached.
Options dialog: a higher number of items for the quantitaiton mode can be seen at a time (20 instead of 8).
Minor corrections to the headers for the recalibration report (menu File/Export Recalibration Report).
More decimals were added for recalibration constants. Significant digits for FT data can be the 8 or more.
Minor changes in options dialog: size changes, item rearrangements, text changes.
Some menu items in the Protein List window got a new name.
When opening the containing folder for a Mascot result file or raw file (main window, context menu) the first existing containing folder is now opened if the file does not exist.
Added to default definitions for MGF file generator. A problem during parsing of the Mascot result with the output from DTASC and the option "Newer DTASuperCharge..." has been dealt with. The option was split into two and you can use the "... v.1.18 ..." for these kind of Mascot result files. The real problem is with DTASuperCharge, but MSQuant has now been adapted to work around the problem.
The progress display during parsing is back in business. It was broken on 2007-10-10. As a result the application is no longer frozen during parsing - you select menu items or open another parse.
The MS3 spectra are again displayed as expected, not staying with the zoom for the MS2 spectrum.
In the export of quantified peptides from the Quantitation window the slope and offset recalibration constants were swopped.
Some fragment masses were computed incorrectly for peptides where the modification does not affect the entire peptide, e.g. terminal modification. For terminal modifications the masses of yN and bN were incorrect. As those masses were not used this bug was harmless. Symptom was an ASSERT during PTM scoring for peptides with terminal modifications.
Can now handle more than 8 phosphorylations in total... (e.g. 3 pST and 5 pSTY - or 11 pST). Such a peptide may take longer to PTM score than the remaining lifetime of our Universe, but that is a separate problem. Sample peptide: K.ALTSATIEDSMTQVMSSSRGPSPDQSTMSQDISTEVITR.L,9026-9064 + Deamidated (NQ); 11 Phospho (ST); 3 PhosphoIntact (STY); 2 Label:13C(6) (R) Symptom: attempting to open a protein where such a peptide would be displayed resulted in the infamous generic failure dialog: "... Problem opening the raw data file (wiff, raw or idx). Likely reasons: 1. raw file mode (Tools/Options) is Analyst or Micromass for a .raw file", with this specific message: "System.IndexOutOfRangeException: Index was outside the bounds of the array."
For QSTAR combined data sets the spectra for peptides can now again be displayed without this interruption: "PIL ASSERT. data_setWiffFileName() called more than once." This problem was introduced on 2007-08-08, v. 1.4.2b6.
2008-02-04. Updated:
N15 section.
Separate packages for Mascot 2.1 and for Mascot
2.2. With Mascot 2.2 it is much simpler to use N15
labeling with MSQuant.
2008-01-16. For developers:
Google indexable MSQuant source code (no longer available).
2007-10-11.
Development (alfa) version of MSQuant:
1.4.3a29 (11.2 MB).
(Is in the 7-Zip format, not ZIP.
The 7-Zip software is
open source and an
installer is available).
Version 1.4.3a24 was broken for QSTAR quantitation. This has been fixed.
In the recalibration visualisation window: median error in 100 Th mass windows. This makes it easy to spot any residual systematic error after recalibration or any systematic error before recalibration. Sample screen-shot (10 KB). (was reduced to 16 colours so the colour gradient is not exactly the same)
Quantitation is somewhat faster and somewhat more memory efficient (display update rate was decreased).
Quantitation now again works for QSTAR data.
The option "Only highest scoring uniquely modified" in the peptide filters now works again; peptides that should have been excluded could turn up in e.g. the export.
2007-10-03.
Development (alfa) version of MSQuant:
1.4.3a24 (no longer available) (11.2 MB).
Version 1.4.3a21 was broken for QSTAR data. This has been fixed.
Binning of the mass errors in the recalibration visualisation window. It includes information about what percentage of the displayed peptides will be included with more narrow mass accuracy settings in the Mascot search. If the peptide filter is set to display all peptides then it is also easy to see that the false positives are evenly distributed (in constrast to gaussian for the true positives). Sample screen-shot (13 KB). (was reduced to 16 colours so the colour gradient is not exactly the same)
none
Can now again open the Protein Validation window for QSTAR data.
2007-10-03. For developers:
7-Zip package for MSQuant v. 1.4.3a24
(0.6 MB) with source code and other files.
New files: SDUPkeyObserver.vb, AnalystSpectrumMarking.vb, overlaySpectrumMarking.vb, SDUPspectrumMarking.vb, ZedGraphSpectrumMarking.vb, frmRecalibrationVisualisation.Designer.vb, frmRecalibrationVisualisation.vb, frmZedGraphTryout.Designer.vb, frmZedGraphTryout.vb and frmZedSpectra.vb.
2007-09-27.
CEBI's version of the MSQuant settings file "new_MSQ_quantitationModes.xml",
updated for MSQuant 1.4.3a21 (terminal modifications and ICAT/HysTag mass differences):
Contains definitions for modifications and
for quantitation modes commonly used at CEBI.
Tips:
2007-09-27.
Development (alfa) version of MSQuant:
1.4.3a21 (no longer available) (11.2 MB).
Good news for Micromass users: the dependence on the
Finnegan software has been eliminated. XCalibur is
no longer required to be installed in order to use
MSQuant with Qtof data!!
The problem with the C13 feature in Mascot has been
fixed.
Native support of terminal modifications. In constrast to
the work-around it
no longer misses some amino acids (e.g.
MRKWP),
the 30 modification site limit for PTM
scoring is much less of a problem and the
number of combinations for PTM scoring are
much less (higher speed and higher memory
efficiency).
How to specify N-term modification for a peptide:
<startPosition>1</startPosition>
<endPosition>1</endPosition>
How to specify C-term modification for a peptide:
<startPosition>-1</startPosition>
<endPosition>-1</endPosition>
Automatic C13 correction: if the mass difference between the Mascot calculated mass (neutral) and the measured mass (+1 Da or +2 Da for C13 peptides) is greater than about +/- 0.5 Da then the measured mass (and corresponding measured MCR) is adjusted by the nominal mass difference times the C13- C12 negative mass difference, e.g. -2.00670965 Da for a 2xC13 peptide. This may cause problems for recalibration if you have searched with a precursor mass accuracy of e.g. +/- 1.3 Da. In that case it is best to restrict peptides for recalibration to +/- 0.4 Da (or lower). (ppm value: compute for lowest precursor MCR.) Note that the measured mass and measured MCR for the C13 corrected peptides are ***permanently*** changed and no longer correspond to the values in the Mascot result file.
Added y-values major gridlines for the recalibration visualisation window.
Now uses the open-source software Zedgraph to display Micromass spectra. There are a few cosmetic problems with the labels. This will be removed in a later version. Thus XCalibur is no longer required to be installed in order to use MSQuant with Qtof data.
Very important if you use HysTag or ICAT: the value of the field "massDiffFromBase" is now always that - a mass difference. Prior to this version MSQuant would use the value as an ***absolute*** residue mass if it was high enough (greater than 120 Da). The mass difference is relative to Cysteine native if it is a high value (HysTag and ICAT) and relative to Carbamido- Cysteine if it is a low value (e.g. N15). This distinction will eliminated when MSQuant is able to read the fixed modification from the Mascot result file and no longer needs to make assumptions about the modification for Cysteine.
If the raw file type is changed (e.g. from Qtof to LTQ-FT) then the quantitation window settings are now also changed. Previously the quantitation window settings would only be set at program startup.
For PTM scoring fragment spectrum display: the correct QSTAR spectrum is now displayed if it is not the first fragment spectrum, e.g. "experiment 3" or "experiment 4".
2007-09-08. For Qtof/Micromass/MassLynx and QSTAR/Sciex/Analyst QS 1.1 (or later) users: see the notes in the section "Combining several raw spectrum files" (close to the end of this page).
2007-09-07.
Development (alfa) version of MSQuant:
1.4.3a7 (11.2 MB).
The C13 problem can now be worked around, see below.
The built-in recalibration process is now visualised (sample). This makes e.g. the problem with the Mascot 2.2 C13 feature very apparent. It is displayed: a. At the end of the parse. For all peptides (in all proteins). b. From the Protein List window, menu Automation/Recalibration Visualisation. It works on the protein selection.
(Controls for recalibration visualisation: a. Resizing the window works! (when the window is not maximised). b. Rotate mouse wheel: zoom in / out. c. Drag out rectancle (with mouse): zoom to that area. d. Press the shift key. Cursor changes to a "hand" and panning is then possible. e. Hover the mouse over a point. Then the query number, peptide sequence, Mascot score, charge and protein number are displayed. f. Right click in spectrum/Undo All Zoom;Pan: returns to original plot. g. Right click in spectrum/Un-Zoom or Un-Pan: back to previous zoom/pan. h. The peptide filter can be used to restrict the plotted peptides. )
(Tips for recalibration visualisation: a. If you set the peptide filter to a minumum score of 30 then only the peptides used for recalibration will be displayed (if there are not too many). )
The set of peptides used for recalibration can now be set (through a peptide filter). An empty set will effectively turn off recalibration. The filter can also be used to prevent the C13 peptides from destroying recalibration (set a required mass accuracy that will exclude them, e.g. -/+ 500 ppm).
The standard shortcut key, Enter, corresponding to double-click now works in the peptide list in the Quantitation window.
A new field, "GUIdoShow", has been added to the quantitation mode definitions in settings file "new_MSQ_quantitationModes.xml" to enable/disable display of it in the Options dialog. Sample: <GUIdoShow>False</GUIdoShow> This makes for displaying only those that are actually used. This new field can added to an existing settings file. The same effect can achieved by simply deleting quant modes, but this way allows external tools to change it and in the future it may be possible to so also in MSQuant.
Keyboard shortcut for export...
Conditions for which peptides to use for
different things (e.g. validation during
parsing) have been generalised into a peptide
filter, taking items from 4 different
places (
peptide modification filter [menu Tool/Options],
peptide validation [menu Tool/Options],
peptide values filter [menu Tools/Peptide Filters] and
verified/quant filters
[Protein list window, menu File/Export Proteins;Peptides].
This much broader peptide filter is
available in the 4 different places as well
as in 2 new places: for recalibration and for
recalibration visualisation.
All peptide filters are remembered across program restarts.
Statistics are no longer available about how many peptides were not validated due to too high mass error.
A further condition for validating a protein during parsing is that at least one peptide must be validated.
In Tools/Options the label and possible values for what is different file formats (Analyst QS 1.1/2.0 vs. MSQuant classic) now instead refer to which software generates the MGF file. This is (hopefully) easier to understand for users.
The program default for the raw file type is now LTQ-FT (was QSTAR). This change is only important when MSQuant is initially installed.
If the file dialog for selecting a Mascot result or a raw file is dismissed with Enter then a parse (of some unrelated data set) is no longer initiated.
Saving (to a MB3 file) no longer fails if the "Remove Peptides for good" command has been used previously.
2007-08-20. Note: the new C13 feature in Mascot 2.2 ("# 13C") does not work at all with the current version of MSQuant (as the reported measured value is with C13 and the reported theoretical value is without). Recalibration will be completely wrong and thus the quantitation result will incorrect too. A new version of MSQuant that addresses this problem will be released soon (order of weeks).
2007-08-20. For developers:
7-Zip package for MSQuant v. 1.4.2 final
(1.8 MB) with source code and other files.
2007-08-10. CEBI's version of the MSQuant settings file "new_MSQ_quantitationModes.xml". Contains definitions for modifications and for quantitation modes commonly used at CEBI.
2007-08-10.
Third official release
of MSQuant!!!. Version 1.4.2.
Installation/usage notes:
2007-08-08. New beta version for MSQuant v. 1.4.2: 1.4.2b6 ( 0.3 MB). 53 hours remain of the beta testing period.
none
PTM scoring now work for QSTAR/Sciex/Analyst and Qtof/Micromass/MassLynx in all aspects (not only manually from the Protein Validation window). When started from the Protein List window and going to the next or previous PTM combination (from the Protein Validation window).
The Protein Validation window can now again be opened without error for Qtof/Micromass/MassLynx. This was broken with on 2007-07-11, corresponding to v. 1.4.2a23.
2007-08-08. For developers:
7-Zip package for MSQuant v. 1.4.2b5
(1.8 MB) with source code and other files.
New files: AnalystCOM.vb, QS11analystCOM.vb and QS20analystCOM.vb.
New approach for COM components (for Analyst only and for v.2.0 and v.1.1 in this version of MSQuant): now references several for each vendor, one for each significant version of the COM component(s). The corresponding interop DLLs are now created by a script ("Vendor COM versioning.bat") using Tlbimp and Aximp instead of using Visual Studio. Instead the generated Interop DLLs, with version numbers in the file name, are referenced directly in Visual Studio ( QS11.AxInterop.GraphControlLib.dll, QS11.Interop.ExploreDataObjects.dll, QS11.Interop.GraphControlLib.dll, QS20.AxInterop.GraphControlLib.dll, QS20.Interop.ExploreDataObjects.dll and QS20.Interop.GraphControlLib.dll. ). If you don't want or need a particular COM type or versions it is now relatively easy to leave them out as the references to them are much fewer than before (for now only true for QSTAR/Analyst). The dependencies to the Analyst COM components are now isolated to the derived classes of AnalystCOM.vb. This scheme will be extended to Analyst QS 1.0, Finnigan and Micromass, but not before 1.4.2 is released.
2007-08-03. New beta version for MSQuant v. 1.4.2: 1.4.2b5 ( 0.3 MB). 175 hours remain of the beta testing period.
To export: number of computed PTM combinations.
PTM scoring is now computed for modified peptides where all sites are modified (no doubt about the sites).
The parse rule for the elution time for QSTAR/QS 1.1 now matches any number of white spaces instead of a single white-space. Symptom was: "Problem extracting information from the tooltip section of the mascot result file"
During parsing it is now checked if a modified peptide contains one of the amino acids from the matched modification (this is sort of an incorrect definition of a modification). This, among other things, prevents problems later with PTM scoring.
During program startup it is now checked if the ID and if the match string of all defined modifications in settings file new_MSQ_quantitationModes.xml are unique. This (probably) prevents an "index out of range" exception during PTM scoring. (at this time it is not understood exactly why this is the case).
During program startup it is now checked if any of the prefix or postfix strings for the defined modifications in settings file new_MSQ_quantitationModes.xml contain uppercase letters. This prevents an ASSERT during PTM scoring.
2007-07-30. New beta version for MSQuant v. 1.4.2: 1.4.2b3 ( 0.3 MB). 260 hours remain of the beta testing period.
To export: wether a peptide is used in the protein quantitation result or not.
None.
For a reopened Quantitation Window: the protein quantitation values are now updated when a peptide is clicked on (or off). It used to work only in the initial Quantitation Window where the quantitation was done.
When a Quantitation Window is reopened: it is now indicated wether or not a peptide is used to compute protein quantitation values (before it was almost always on).
More of the scrollbar in the Protein Validation window is now visible (and therefore much easier to use...).
All of the third label in the Spectrum Reduction parameters dialog is now visible.
2007-07-26.
Public
beta testing programme for MSQuant v. 1.4.2:
1.4.2b1 ( 11.2 MB).
The beta testing programme will last 334
hours, starting from 2007-07-26T18:00:00Z.
Please report bugs as soon as possible.
Please note in particular the first mentioned bug
fix below...
Additions, changes and bug fixes since v. 1.4.1 (2007-03-06):
Support for Mascot 2.2 output. Please note: the default modifications (e.g. SILAC) in Mascot 2.2 are quite different from the ones previously used. Thus the file "new_MSQ_quantitationModes.xml" must be adjusted accordingly.
New feature to allow Analyst QS/QSTAR users to bypass running a script and use the output of Mascot.dll directly. Some parse rules are now defined outside the program, in the settings file "new_MiscOptions.xml" and a particular set (e.g. for later versions of Mascot.dll for Analyst QS) can be selected in the options dialog. It is the rules used to extract information from what was in the 'TITLE' lines in the input file for the Mascot, e.g. from "TITLE=Elution from: 31.16 to 31.16 period: 0 experiment: 4 cycles: 1". Note however that in this version definitions in "new_MiscOptions.xml" are for information only; at this point it is not possible to add new defintions and get it recognised by MSQuant. (May be implemented later: if you have software that creates TITLE lines with a different format than the MSQuant standard or later versions of Mascot.dll for Analyst QS then it may or may not be possible to add new defintions for it. The easiest way to get the definitions is to rename "new_MiscOptions.xml" and restart MSQuant. This creates a new "new_MiscOptions.xml" that you can then edit.)
Auto-doc (tm). Can now generate a report containing peptide information and its spectrum for all verified peptides of the selected proteins. It is intended for journal (e.g. MCP) requirements for documentation of raw spectra and matching ions. Output from MSQuant is in the DocBook format. This format can be converted into other formats, including HTML page(s) and PDF. Being a text format it also allows some postprocessing (e.g. reordering or leaving out information) before being converted to HTML or PDF. Preview of Auto-doc, HTML (for an early version of the Auto-doc feature). Preview of Auto-doc, PDF (for an early version of the Auto-doc feature). For your own data use the application "XMLmind FO Converter". Please refer to the "Tips" section above. To generate the DocBook files in MSQuant use the new menu command "Automation/Report..." from the Protein List Window.
In the Protein List window and the Quantitation window the columns with quantitation information can now be sorted...
For MS3 scoring: it is now possible to set the mass tolerance for the fragment ion matching (Protein Validation window, menu Protein/Peptide; Spectrum Reduction Parameters). This is also applied to PTM scoring and to the normal display of matching fragment ion peaks for a peptide. Note : the settings are not remembered by the program. They must also be set for each Protein Validation Window (they are not currently program wide settings).
Going one level down from the identification spectrum (to MS3) is now possible. (Protein Validation window, menu View/Down one spectrum level)
PTM scoring is now possible for non-Finnigan data.
PTM scoring can now work with amino acids in the peptide that are affected by more than one modification, e.g. pSTY and piSTY or terminal modifications work-around and any other modification. It has a new menu command, "PTM score - broader". The old PTM score is still available for reference.
The modification filter dialog can now handle a larger number of modifications.
Error reporting and error handling is now better if MSQuant runs out of memory while ***opening*** a Mascot result file for parsing (opening happens in the very beginning of the parsing). Example: after parsing "Secretome_d0_1_4.htm" (162 MB) for the first time MSQuant memory consumption is 482 MB. Parsing it for the second time may either result in an out-of- memory condition or in some cases it works (memory consumption 948 MB !!!). The out-of- memory condition resulted in this message: "PIL ASSERT. Select Case never fall-through.".
The "checked" state of a peptide in the Mascot Result file (.HTML) is now again parsed (from 2004-06-17/Mascot 2.0 until now it was considered always checked).
(Identified) SILAC pairs are no longer excluded from the Quantitation window. (in the same raw file, with the same charge and with the same modification state (mass)) Note: identified (by Mascot) SILAC pairs, not SILAC pairs in the MS data. (Fixed 2007-06-20.)
The options for including bold black peptides now work... They have never worked in the entire (or almost entire) life of MS Parser/MSQuant (!).
Now works for MS3 spectra and XCalibur 2 SR2 or later (XCalibur 2 SR1 worked OK; in SR2 two "cid"s are added to the spectrum headers - e.g. "ITMS + c NSI Full ms3 567.24@cid30.00 51808@cid30.00 [130-1050]"). The error message was misleading: "Unknown spectrum type, could not be derived from spectrum title (looking for ms3 or ms2) 'ITMS + p NSI d w Full ms3 948.07@cid30.00 1539.77@cid30.00 [410.00- 1550.00] '. The configuration file new_spectrumClassification.xml does not contain information to recognise the spectrum type, MS or MS/MS. Edit new_spectrumClassification.xml."
Recalibration now always represent the entire observed peptide mass range (in extreme cases, for very large number of peptides for the first protein, recalibration was broken). Example: the first 300 peptides have nearly the same mass, e.g. are only in the mass range [728.408539 - 733.419388 Th]. This can happen if the first protein has a very large number of peptides. MSQuant is now using (approximately) only the highest scoring peptide mass for each nominal mass; thus no particular mass or mass range has higher weight than others.
For a quantified peptide in the Quantitation Window: clicking off and clicking on did not have the expected behavior (e.g. protein ratios would stay at the ***clicked off*** values). This bug was probably introduced at 2006-10-10.
Some quantitation values in the export for a non-quantified peptide are no longer incorrectly using the value from some quantified peptide... Sample of this bug.
The menu command "Automation/Zap intermediate quantitation results" no longer deletes some ***peptide*** quantitation values (that it should not delete).
Fixed: display of the correct fragment spectrum for all versions of Analyst QS and for Mascot result files generated with the help of all versions of Mascot.dll.
Spectrum annotation (fragment ions) no longer disappears when going one level up and then one level down. (Protein Validation window, menu View/Down one spectrum level)
When there is no MS3 score the contribution is now correctly set back to zero. This can happen if MS3 scoring on different PTM combinations, e.g. first MS3 scoring on a combination where a fragment mass matches the MS3 precursor mass and then MS3 scoring for a combination where no fragment mass matches.
No longer crashes if regional settings is Norwegian (and possibly others)... Those where "Digit grouping symbol" is not "."
For MS3 scoring on PTM scored peptides: a bug was fixed that in rare cases made MSQuant crash (index out of range exception) or return incorrect results. It happend only for automation/MS3 and could not be reproduced by manual operations with MS3 score. It also depended on the order in which the MS3 scoring was done; even on which set of proteins was MS3 scored. This bug probably caused a mass difference of -42 Da to be used in some cases (depending on the defined modifications, etc.). This bug may have been introduced on 2006-08-01. Impact: low; the MS3 score could be incorrect in some cases, but only for a few peptides and only if PTM scoring was performed first and only if PTM scores were very low (below the display threshold).
If the name for the mb3 file to be saved contains a dot (".") then the resulting file on the disk will now always have the MB3 file extension. In the past it would not and therefore not show up in the dialog for opening a MB3 file.
2007-07-05.
Development (alfa) version of MSQuant:
1.4.2a23 (11.2 MB).
As from now on the software is placed in the 7-Zip format, not ZIP.
The 7-Zip software is
open source and an
installer is available.
Other archive software may be able to decompress the 7-Zip files.
I apologise for any inconvenience.
Installation: you must use the
MSQuant installer to install this version.
The unfortunate installer glitch of the previous
version has been fixed. The default tooltip format
after installation is now the most common, the
MSQuant standard format (not QS 1.1 or later). Plus
minor changes, some user options were removed.
2007-06-29.
Development (alfa) version of MSQuant:
1.4.2a22 (no longer available) (11.1 MB).
Installation (IMPORTANT !): You
***must*** use the installer to install this version
and due to an unfortunate installer glitch you must
also do this (even if you don't use QSTAR data):
make a copy of the file
"QS20.Interop.GraphControlLib.dll", rename the copy
to "GraphControlLib.dll" (check: the file size is 88
KB - it is easy confuse this file with the two other
files with similar names).
Should now truely really work (but remains to be
fully tested): display of the correct fragment spectrum
for all versions of Analyst QS and for Mascot result
files generated with the help of all versions of
Mascot.dll.
2007-06-21. Development (alfa) version of MSQuant: 1.4.2a19 (11.5 MB). Should now really work (but remains to be tested): can directly parse output Mascot result files that were generated with the help of the Mascot.dll for Analyst QS 2.0 (no longer needed to run a script). PTM scoring is now possible for non-Finnigan data (but remains to be tested). (Note: the "TITLElineParseDefinitions" section in settings file new_MiscOptions.xml is written, but in this version of MSQuant the content of that section is ignored when the program reads the file - instead the program defaults are used.)
2007-06-19. Development (alfa) version of MSQuant: 1.4.2a18 (11.5 MB) (no longer available). Now works for Analyst QS 2.0: can directly parse Mascot result files that were generated with the help of the Mascot.dll for 2.0 (no longer needed to run a script), the correct fragment spectra are always displayed and the installer installs the correct Interop files (Interop.ExploreDataObjects.dll). Note: the "TITLElineParseDefinitions" section in settings file new_MiscOptions.xml is written, but in this version of MSQuant the content of that section is ignored when the program reads the file - instead the program defaults are used.
2007-06-15. Updated: Qtof sample data. See section "Getting started" for details.
2007-06-06. Development (alfa) version of MSQuant: 1.4.2a14 (11.1 MB). Now again reads the content of settings file "new_MiscOptions.xml"... Particulary important for the quantitation window width for FT data !!! This was broken on 2007-05-02 - corresponding to 1.4.2a13.
2007-06-05. Note for Qtof: MSQuant does not (currently) work with MassLynx 4.1. For the time being you must use MassLynx 4.0 instead.
2007-05-18. Development (alfa) version of MSQuant: 1.4.2a13 (11.2 MB). Now works for MS3 spectra and XCalibur 2 SR2 or later (XCalibur 2 SR1 worked OK; in SR2 2 "cid"s are added to the spectrum headers). For MS3 scoring on PTM scored peptides: a bug was fixed that in rare cases made MSQuant crash (index out of range exception) or return incorrect results. Recalibration now always represent the entire observed peptide mass range (in extreme cases, for very large number of peptides for the first protein, recalibration was broken).
2007-05-18. For developers:
source code and other files for MSQuant v. 1.4.2a13 (1.0 MB).
For FastSerializer.cs please refer to the article
Optimizing Serialization in .NET - part 2.
The source code from that article can be used unchanged.
2007-05-16. DTASuperCharge, version 1.18 (10.6 MB) - an application for converting one or more Finnigan .RAW files to Mascot search input files in a format suitable for use with MSQuant. Now works for MS3 spectra and XCalibur 2 SR2 or later (XCalibur 2 SR1 worked OK; in SR2 2 "cid"s are added to the spectrum headers).
2007-05-16. For developers: Source code and other files for DTASuperCharge v. 1.18 (0.14 MB).
2007-05-11. Please note: MSQuant can only parse Mascot result files (.html) saved with Internet Exploiter 6 or earlier. It does not immediately work with these browsers: Internet Exploiter 7, Opera, FireFox, Netscape and others. There is however a work-around: a utility (.NET application) is available to convert a Mascot result file to the form of HTML that MSQuant expects. Use the button "Convert to MSQuant Readable File...". In the future MSQuant will be made browser agnostic.
2007-05-03. Note: if you use PTM scoring with MSQuant v.1.4.2a6 then prefix and postfix strings for modifications must not contain uppercase letters. This is a restriction, not a bug. This restriction may be lifted in a future version.
2007-04-24. Development (alfa) version of MSQuant: 1.4.2a6. Support for Mascot 2.2 output. A detailed description of other additions, changes and bug fixes in this version will be released with the first beta version of MSQuant 1.4.2.
2007-04-18. For developers: use of CVS has been discontinued. ZIP package for v. 1.4.1 final (0.9 MB): source code and other files.
2007-03-15. DTASuperCharge, version 1.17 (10.6 MB) - an application for converting one or more Finnigan .RAW files to Mascot search input files in a format suitable for use with MSQuant. Note 1: XCalibur must have been installed with the "XDK" option checked !!!!! Note 2: this application is dependent on some other application to generate input DTA files, e.g. extract_msn.exe (part of Bioworks). See below, section "Preparing input files for the Mascot search engine", subsection "LTQ-FT" for details.
2007-03-06. Second official release of MSQuant. Version 1.4.1.
2007-02-26. New beta version for MSQuant v. 1.4.1: 1.4.1b4.
Somewhat more memory efficient.
The protein score no longer includes peptides that are excluded due to the SILAC rule (fixed modification condition and from the same dish).
MSQuant can now really truely 100% handle more than 3 SILAC dishes. The headers for export of proteins lines are now correct; no longer fixed to triple encoding.
2007-02-26. The two major bugs have now been described, see the 2007-02-02 entry.
2007-02-15. MSQprojectFiles,2007-02-15b.zip. For MSQuant developers only. Updated sample project files for users of Visual Studio .NET, valid for version 1.4 final or later of MSQuant. Make sure to follow the instructions in MSQprjFIlesReadMe.txt (!!).
2007-02-07. There has been reports of trouble with upgrading to XCalibur 2.0 SR2, e.g. from XCalibur 2.0 SR1. Apparently the spectrum headers (for the same .RAW files) are now different. This has to be investigated. It may be necessary to change the content of settings file "new_spectrumClassification.xml".
2007-02-07. 121 hours remain of the beta testing period. No new bugs have been reported - so this version may be bug-free!
2007-02-02. Public beta testing programme for MSQuant v. 1.4.1: 1.4.1b2.
Compiled as 32 bit. MSQuant should now always run as a 32 bit application on a 64 bit operating system, e.g. "Windows XP Professional x64 Edition". This has not been tested, though.
Two (years old) major bugs in quantitation were fixed (they were somewhat dependent; the second masked the first):
1. Quantitation window: the threshold used
for the 20 percent rule is now local to
the (computer-) selected LC peak instead
of using the highest LC peak (global) in
the quantitation time window.
The 20 percent rule ensures that weak
spectra are left out of computations for
the peptide quantitation result.
Impact: no impact if the LC peak with the
MS- MS event was the highest peak in
the window. Otherwise the threshold
would be too high and some or all
spectra were ***not*** used for
quantitation; leading to no
quantitation result or to a result with
worse statistics than needed.
2. The checked state of spectra was not
consistent with what spectra were used for
computing the peptide quantitation result.
The state displayed was
before the 20 percent
rule on the LC peak was applied.
Impact: fewer spectra were used than
displayed. Very confusing for the user
and incorrect result compared to the
user selection.
No impact if the user
clicked or dragged the mouse in the LC
peak window in the lower right. In this
case the display and the internal values
became consistent.
For old versions you can verify this bug
by using menu File/"Export peptide with
spectrum list". With the new version you
can verify that it is now consistent...
Some minor bugs in quantitation were fixed.
For combined files, entry to the Quantitation window: some identified peptides are no longer excluded by inserted peptides.
2007-01-26. Version 1.4 of MSQuant has been withdrawn.
2007-01-11. First official release of MSQuant!! Version 1.4. (no longer available). This version includes the phosphorylation site scoring that was crucial to our Cell paper, "Global, In Vivo, and Site-Specific Phosphorylation Dynamics in Signaling Networks" (full text, PDF) by Jesper V. Olsen, Blagoy Blagoev, Florian Gnad, Boris Macek, Chanchal Kumar, Peter Mortensen, and Matthias Mann. 2006. Full text, HTML (may not be available). Abstract.
Any number of SILAC dishes for quantitation can now be handled; please note that column numbers in the export are now dynamic (are dependent on the number of SILAC dishes) and that some columns have been phased out; probably requiring changes to various scripts that process MSQuant export files.
PTM scoring - scoring of the modifications on different locations in the peptide. This works not only for phosphorylation (see above), but for any modification and can be used to get the correct fragment ion mass to be computed in the Protein Validation window. This is required if a peptide is only partially modified (e.g. one Methionine is oxidised according to Mascot, but there are several in the peptide sequence.)
The quantitation integration window (indicated by the blue lines in the lower left of the Quantitation Window) is now auto-centered on the MS-peak. This is useful when there is a significant space charge effect in full scan FT spectra (Finnigan data).
The quantitation signal thresholds are no longer hard-coded. They can now be defined by the user, currently by editing the file "new_MiscOptions.xml". The new fields are quantThreshold_QSTAR, quantThreshold_LTQFT and quantThreshold_Qtof but it is safest to let MSQuant generate a new version of this file: rename file "new_MiscOptions.xml", start MSQuant, exit MSQuant, edit the new file and transfer important settings/values from the old file.
Quantitation values for all isotopes are now displayed for each spectrum in the Quantitation window.
Retention time correlation can now be done at any time, optionally using the LC profile time centroid values instead of MS-MS event time, using any sub-set of the proteins. Use the new menu command Protein List Window/Automation/"Retention Time Correlation". You may want to first remove the existing inserted peptides using the new menu command Protein List Window/Automation/"Remove Peptides Inserted by Retention Time Correlation" (before or after quantitation).
Added option for only retaining the highest scoring unique modified peptides (main window, menu Tools/"Peptide filters").
Menu command to open the folder in which MSQuant is installed; main window, menu Utility/"Open MSQuant folder". For e.g. easy access to editing the setting files, "new_MSQ_quantitationModes.xml", "new_MSQ_correlationSettings.xml", "new_MiscOptions.xml" and "new_spectrumClassification.xml".
Find command, for the protein list. It can currently only search in the protein
