Vendor, Instrument & Acquisition neutral analysis 

MassMetaSite is the third-party software that can process most of the vendor proprietary data formats. 

MassMetaSite is a vendor neutral application that can process data obtained from different vendor instruments and acquisition modes. The program translates using the file converter from all the different formats to an internal one used in the computations, standardizing the multiple data into a single format. 

List of the multiple vendors, acquisition modes and instrument that MassMetaSite can process: 


Acquisition modes: 

  • Auto MSMS 
  • All ions


  • QTofs: 
    • 6545 LC/Q-TOF 
    • 6546 LC/Q-TOF 
    • 6530 Q-TOF LC/MS 
    • 6550 iFunnel Q-TOF LC/MS 
    • 6560 Ion Mobility LC/Q-TOF 
  • Triple Quads: 
    • 6470B Triple quadrupole LC/MS 


Acquisition modes: 

  • DDA 
  • DIA 
  • Ion Mobility 


  • Compact, Impact and Maxis 
  • Tims TOF 


Acquisition modes: 

  • DDA 
  • SWATH 


  • Triple TOF® 
  • Triple Quad™ LC-MS/MS Systems 


Acquisition modes: 

  • DDS 
  • All Ion Fragmentation 

Instruments tested:

  • Orbitrap 
  • IonTrap 
  • Q-Exactive 
  • Triple Quad 


Acquisition modes: 

  • DDA 
  • MSe 
  • HDMSe 

Instruments tested:

  • Xevo G1 G2, G2-XS 
  • Synapt Ga, G2-Si 
  • Vion IMS 
  • BioAccord 

Control system:

  • UNIFI 
  • MassLynx 
Multiple Signal Analysis: UV, fluorescence and Radio 

MassMetaSite can not only process MS signal from multiple vendors, instruments and acquisition modes it can also process data from other signal types like Ultraviolet, Fluorescence and radio chromatograms. The system performs a independent peak finding for each of these signals and automatically align the signal in the analog channel and the MS signal using the parent chromatogram as the refence one. All the different signal types can be also used to filter the peaks depending on the percentage of total Area found. 

  • In the case of Ultraviolet (UV), the system used Diode Array data and the user can select the wavelength to compute the area or it can use 2 different algorithms to find out the most convenient wavelength considering the maximum absorbance and the selectivity of the signal. 
  • In the case of Radio Chromatogram, the system can use the signal that may come in the analog channel of the acquisition files or that have been processed by using the program Laura from the Lab logic. In the latest case, the user can use directly the measurement file formats and the installation of the Lab logic libraries is necessary. 
  • In thcase of fluorescence signal type, different degrees of signal smoothing can be used.  
Chemical structure diversity

MassMetaSite is using the mol of sdf file as the standard format to input the structure for small and macromolecule. The system is accepting both V2000 and V3000. Also, the system can deal with different stable and unstable isotopes. In addition, MassMetaSite provides a tool to draw the chemical structures that is flexible to consider isotopes, charges, etc. 

Brief description of the mol format: