System Requirements

  • Windows Vista / 7 / 8

    Windows platform is required for the conversion of raw MS data file to a universal file format by a windows executable program, msconvert, that is packed with NitroQuant. Support of other platforms will be included in next update.
  • Java Version 7

    The latest version of Java is required for running NitroQuant online.
  • Permission to Load Data Files

    During program launch, permission to load data files from hard drive need to be granted.
  • Administrator Right

    During the quantification process, intermediate files like .mzXML will be created. To store these files to your hard disk drive, administrative rights is required.


Launch NitroQuant





Introduction of NitroQuant

NitroQuant is a program tailored to analyse 15N metabolic labelling data. User only need to key in an in-house determined incorporation rate to kick start an analysis. This program take the entire elution profile of a peptide into account when calculating the ratio of light to heavy peptide. User can visualize the integrated peptide envelope in an interactive graphical windows. Any parameter that affect the ratio can be changed on the fly (e.g. scan begin/end). Compared to other third party quantification software like MSQuant and TPP, NitroQuant is the only one that consider the influence of heavy nitrogen incorporation rate.  Failure to consider the rate would give an inaccurate quantification result. NitroQuant core algorithm is implemented in C++ yet GUI is in JAVA. This guarantee a higher processing efficiency while able to give user a rich interactive experience.




Incorporation Rate InputIncorporation Rate Input

NitroQuant allow you to input the heavy nitrogen incorporation rate determined in your lab

Parameters AdjustmentParameters Adjustment

Parameters affecting the ratio of each peptide can be changed individually after initial quantification process has finished. New ratio will be calculated immediately.

Storage Intermediate FilesStorage Intermediate Files

Intermediate files generated during the quantification process are stored automatically . This ensure a faster response in repetitive analysis.


Quantification results can be plotted in three different ways: Integrated Intensity v.s. M/Z, Intensity v.s. Elution Time and 3D plot of Intensity, M/Z and Elution Time

Simultaneous Analysis of Multiple DatasetSimultaneous Analysis of Multiple Dataset

NitroQuant allow more than one quantification processes be run in parallel. This give you a higher throughput in data analysis.

Result ExportResult Export

All result data including data used for different types of plotting can be downloaded through export in excel format

Clear Result PresentationClear Result Presentation

Every detail of a peptide is clearly presented in a tabular format


All graphical display can be zoomed


Preparation before NitroQuant analysis



Convert raw MS data to Mascot Generic Format (MGF)

This step convert your raw data file (e.g. abc.raw) to a format that is searchable by MASCOT. You can use MSConvert packaged in ProteoWizard to finish this task.


Mascot search and result export

Use the converted .mgf file to perform mascot search and export the result in .dat format.


Quantitative peptides ratio with NitroQuant

Rename your .dat  file to the same name as your raw MS data file (i.e. abc.dat) and place them in a same folder under your hard disk root (e.g. C:\myfolder\abc.raw and C:\myfolder\abc.dat). Browse to the locations of these two files and perform quantitation with NitroQuant.