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Tip: Installation on Windows Vista and Windows 7

MSQuant can be installed and work on Windows Vista and Windows 7.

How?

Install it outside of the program files folder (typically folder "C:\Program Files"). For instance in folder "C:\MSQuant".

Tip: v2010-05-25. Download (-999.9 MB).



  • Added: <none>
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  • Bug fixes: <none>

Posted by Peter Mortensen on 2010-05-25T21:07:00+0200

MSQuant: Beta 6 for MSquant v2.0: beta testing unexpectedly continues

A serious problem was discovered in the last moment. Unmodified and N15 labeled peptides could no longer be quantified. After a few fixes it now works for unmodified peptides. It is not known whether it works for N15 (changes have been made for this, but it has not been tested.) The beta testing period continues indefinitely until all serious issues have been resolved. (Beta 5 was only was released to the public.)

MSQuant: v2.0b6. Download (11.9 MB).



  • Added:

    <None>.

  • Changes: <none>
  • Bug fixes:

    Unmodified peptides now enter the quantitation window. And quantitation works for them, at least the Lyris yeast standard data set (double encoding, Lys8).

    A number of crashes in the display of LC profiles were fixed.

Posted by Peter Mortensen on 2010-03-17T20:24:00+0100

MSQuant: Release candidate for MSQuant v2.0: Beta 4

The beta testing period has ended (not really - see newer posting). This version is a release candidate and unless something catastrophic is discovered before 2010-02-25T22:00:00Z the final 2.0 version will be identical to this version.

MSQuant: v2.0b4. Download (11.2 MB).



  • Added:

    In the new LC profile display the LC points used for quantitation are now marked (with black filled circles).

    In the new LC profile display the MS-MS sequencing event (that identified the peptide) is now marked with a cyan vertical line.

  • Changes:

    The maximum time distance for LC peak detection was set back to the previous value (effectively infinite). It was 10 seconds for a while.

  • Bug fixes:

    The Analyst/QSTAR spectrum is now correctly positioned in the Protein Validation window.

    The spectrum markers for Micromass/Qtof spectrum in the Quantitation window are now correctly positioned vertically.

Posted by Peter Mortensen on 2010-02-25T11:02:00+0100

MSQuant: Beta 3 for MSquant v2.0: LC peak smoothing

LC peak smoothing (experimental) has been implemented.

And it is now possible to open a particular MB5 from the command-line or a .BAT file. Precede the full path to the MB5 file with (excluding the quotes): "-bin"

MSQuant: v2.0b3. Download (11.2 MB).



  • Added:

    Smoothing of LC peaks. The quantitation values for peptides and protein are recalculated. Use menu Quantitation/"Smooth LC profiles and do LC peak detection, etc." in the Quantitation window

  • Changes:

    The program no longer quits if no PTM scoring, MS3 scoring, quantiation or export are specified from the command-line. Instead it stays open with the specified opened MB5 file. This allows for fewer manual steps if the same MB5 file is worked on for a long time. E.g. the following can be put in a Shortcut (your paths may vary. Note that the full path to the MB5 file has been quoted as it contains spaces):

    D:\dproj\MSQall\MSQuant\bin\MSQuant.exe -bin "L:\tempCollection\temp20,JBquantTrouble\2010-01-20a,JAB,Quantitation Ratio Oddness\F091498.dat,QUANTMODE_v2.2 DimethylTag,SDUP,quantified q9276,dims defined.mb5"

    Note that it does not open immediately, wait 5-10 seconds. This interval may be shortend in a future version.

  • Bug fixes:

    <None>

Posted by Peter Mortensen on 2010-02-22T15:42:00+0100

MSQuant: Beta 2 for MSquant v2.0: Micromass support

Micromass support is now working. It may or may not be required to register the file DACServer.DLL. Use "cd D:\MassLynx; regsvr32 DACServer.dll" in a command-line window (for MassLynx installed in folder "D:\MassLynx").

MSQuant: v2.0b2. Download (11.3 MB).



  • Added:

    Micromass support has been enabled.

  • Changes:

    <None>

  • Bug fixes:

    <None>

Posted by Peter Mortensen on 2010-02-14T23:20:00+0100

MSQuant: Public beta for MSQuant v2.0 has started!

The public beta testing period for MSQuant 2.0 started today. Any bugs reported will be fixed proptly. The beta testing period will last 12 days and end on 2010-02-24T10:00:00Z.

MSQuant: v2.0b1. Download (11.2 MB).



  • Added:

    Uninstall is no longer required prior to installation, at least not for different versions of MSQuant

    The program can now determine and correct for time shifted LC peaks. Enable it by editing settings file miscOptions.xml. Note however that this is still an experimental feature and there are known bugs that will result in incorrect results for typically 10% of the peptides.

    Good news for owners of computers with low screen resolution: the Protein Validation window and the Quantitation window can now be resized. Note that there are some screen update glitches when the Protein Validation window is initially opened. It can be worked around by opening a peptide.

    In the main/start window there is now an explicit menu item for starting a parse. Previously one had the known that pressing Enter (or double clicking) on an associated item would start a parse. Now it is in writing and discoverable.

    Checking of the quantitation modes definition file, quantitationModes.xml, is now more strict. The quantitation mode ID must now be unqiue.

  • Changes:

    The modification count from Mascot is now used instead of assuming that all amino acids are modified. This enables quantitation of non-SILAC labelling. Note however that the fragment ion masses are not correct in more complicated cases.

  • Bug fixes:

    <To be added>

Posted by Peter Mortensen on 2010-02-11T14:32:00+0100

MSQuant paper: Paper soon to be published about MSQuant

A paper, "MSQuant, an open source platform for mass spectrometry-based quantitative proteomics.", is going to be published soon in Journal of proteome research. Abstract. Full text, PDF (5.7 MB). Full text, HTML (0.5 MB).

MSQuant paper: v2009-11-04. Download (0.2 MB).



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Posted by Peter Mortensen on 2009-11-15T21:31:01+0100

quantitationModes.xml: CEBI's version of the MSQuant quantitation settings file

The latest CEBI version of the MSQuant settings file "quantitationModes.xml" is now available. It was last modified on 2009-03-06 and it contains definitions for modifications and for quantitation modes commonly used at CEBI.

quantitationModes.xml: v2009-03-06. Download (0.01 MB).



  • Added:

    <see change list inside the file>

  • Changes:

    <see change list inside the file>

  • Bug fixes:

    <see change list inside the file>

Posted by Peter Mortensen on 2009-11-14T20:10:55+0100

MSQuant: First public release for v2.0.

This is the first public release on the road to v2.0 of MSQuant. This version is 3.5 times faster for quantitation and about 40% faster for PTM scoring and MS3 scoring. It is also snappier when using manual validation in the Protein Validation window.

MSQuant: v2.0a81. Download (11.2 MB).



  • Added:

    <none>

  • Changes:

    Not really a feature, but quantitation is now 3.5 times faster!

    Not really a feature, but PTM scoring and MS3 scoring is now 40% faster!

  • Bug fixes:

    Fixed in helper application MSRecal: recalibration for Orbitrap was completely and utterly broken.

Posted by Peter Mortensen on 2009-10-08T23:50:00+0200

DTASuperCharge: is now 7 times faster!

Update, 2010-02-06: the new option for preprocessing is broken if "Use charge state from DTA file" in tab "DTA Processing" is turned on. Turn it off (uncheck it).

Otherwise there will be false negative Mascot identifications as some peak lists will not be included.

Update, 2009-12-09: the new option for preprocessing is broken for fragment groups longer than one. E.g. if there are 6 fragment spectra, CID, ETD, CID, ETD, CID and ETD only every second spectrum will be used - leaving out the ETD spectra from contributing to the Mascot MGF file. It has been fixed and the next version will include this fix.

Some unnecessary operations in DTASuperCharge were eliminated and as a consequence a conversion of a raw file is now 7 times faster, from a total runtime of 16 minutes on sample dataset 2 to 2.5 minutes. The download is really for MSQuant - when installed the bundled DTASuperCharge is the new fast one.

DTASuperCharge: v2.0a6. Download (11.8 MB).



  • Added:

    Not really a feature, but is 7 times faster.

    New option for preprocessing, eiiminating the need for ExtractMSN. Thus there is no need for a license for BioWorks. BioWorks has also been discontinued; the only way to get the functionality of ExtractMSN is the EUR 20000 ProteomeDiscoverer.

  • Changes:

    <none>

  • Bug fixes:

    <none>

Posted by Peter Mortensen on 2009-10-08T15:31:00+0200