MS-Deconv Manual

1. About MS-Deconv
    1.1. Supported data types
    1.2. MS-Align+ pipeline
    1.3. Performance of MS-Deconv
2. Installation
    2.1. Downloading MS-Deconv
3. Running MS-Deconv
    3.1. Input
    3.2. Command line options
    3.3. Commands
    3.4. Graphical user interface
    3.5. Output
4. Citation
5. Feedback and bug reports

1. About MS-Deconv

MS-Deconv is a software tool for top-down spectral deconvolution. It first generates a large set of candidate isotopomer envelopes for a spectrum, then represents the spectrum as a graph, and finally selects its highest scoring subset of envelopes as a heaviest path in the graph. In contrast with other approaches, it scores sets of envelopes rather than individual envelopes. MS-Deconv can be downloaded from

1.1 Supported data types

The current version of MS-Deconv works with Thermo raw data.

1.2 MS-Align+ pipeline

The MS-Align+ pipeline for analyzing raw data includes three components: format conversion, deconvolution, and database search.

1.3 Performance of MS-Deconv

See the paper Liu et al. 2010 .

2. Installation

MS-Deconv requires a computer with at least 2 GB memory, a 64-bit Linux or Microsoft Windows operating system, and Java Runtime Environment 7.0.

2.1 Downloading MS-Deconv

Download a JAVA jar file or a Windows executive file at MS-Deconv

3. Running MS-Deconv

3.1 MS-Deconv input

The input file of MS-Align+ is a spectrum file in the mzXML format, which can be obtained by using ReAdW. For example, example.raw can be converted to an mzXML file using the following command:

ReAdW -c example.raw example.mzXML 

3.2 Command line options

To run MS-Deconv from the command line, enter the directory where the MS-Deconv jar file is stored and run the following command:

java -Xmx2G -jar MsDeconvConsole.jar  [options]

Basic options

-o, --output <mgf|text|msalign>
    Specify the output file format: mgf, text or msalign. The default format is mgf. When the resulting file is analyzed by MS-Align+ for protein identification, the format msalign should be used.

-t, --type <centroided|profile>
    Specify the type of the input spectra: centroided or profile. The default type is centroided. Because MS-Deconv employs a simple centroiding method to convert profile spectra to centroided ones, we recommend that the user utilizes other software tools, such as ReAdW, to convert profile data to centroided one, and uses the default type "centroided" in MS-Deconv.

-p, --precursor
    Specify to use the precursor masses of tandem mass spectra in the spectrum data file. If the argument is not used, MS-Deconv deconvolutes envelopes of precursor ions to obtain the precursor masses of tandem mass spectra.

-l, --level-one
    Report deconvolution results of MS1 spectra.

-k, --keep
     Report peaks not in good isotopic envelopes.

-c, --max-charge <integer value>
    Set the maximum charge state of isotopic envelopes. The default value is 30.

-m, --max-mass <float value>
     Set the maximum monoisotopic mass of fragment ions. The default value is 49000.

-e, --mz-error <float value>
     Set the error tolerance of m/z values of peaks. The default value is 0.02.

-s, --sn-ratio <float value>
    Set the signal noise ratio. The default value is 1.

-u, --multiple-mass
     Output multiple possible masses for one envelope.

3.3 Commands

A desktop with at least 2 GB memory is required to run MS-Deconv. To run MS-Deconv, open a console in a Linux platform or a command line interpreter in Microsoft Windows, enter the directory where MS-Deconv jar file is stored, and run the following commands:

Deconvolute centroided data spectra.mzXML to mgf file spectra_msdeconv.mgf

java -jar msdeconv.jar spectra.mzXML

Deconvolute centroided data spectra.mzXML to text file spectra_msdeconv.txt

java -jar msdeconv.jar spectra.mzXML -o text

Deconvolute centroided data spectra.mzXML to spectra_msdeconv.mgf by using orignial precursor masses

java -jar msdeconv.jar spectra.mzXML -p

Deconvolute centroided data spectra.mzXML to spectra_msdeconv.mgf and report results of both MS1 and MS2 spectra

java -jar msdeconv.jar spectra.mzXML -l

Graphical user interface

To run the GUI of MS-Deconv, double-click the downloaded exe file in Microsoft Windows. To deconvolute a spectrum data file, use the button "Open a file..." to select the data file, change parameters if needed, and click the button "Run MS-Deconv" to start deconvolution.


The output file of MS-Deconv is stored in the same directory of the spectrum data file. If the spectrum file name is spectra.mzXML and the output file format is mgf, the output file name is spectra.mgf. The extension of the output file name depends on the output file format.

4. Citation

If you use MS-Deconv in your research, please include Liu et al., 2010 in your reference list.

5. Feedback and bug reports

Your comments, bug reports, and suggestions are welcome. They will help us to further improve MS-Deconv.

If you have any troubles running MS-Deconv, please email us or post your questions at the google group of MS-Deconv and MS-Align+.