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MS Data Processing and Interpretation

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  • MS Data Processing and Interpretation

    Mass Spectrometry (MS), the ions with different mass-charge ratio are separated by the mass analyzer, detected and recorded by the detector, and expressed in the form of mass spectrogram after computer processing. Rich mass spectrum information can be obtained through mass spectrometry, including the composition of various fragment ion elements, and the relationship between molecular ions and fragment ions, fragment ions and fragment ions according to metastable ions, the relationship between molecular cleavage mode and molecular structure. Through the m/z peak and its intensity, the relative molecular mass of organic compounds, the chemical formula and structural formula of the compound can be determined, and quantitative analysis can be performed.

    The mass spectra of organic compounds are ever-changing, and some compounds only differ in the position of the substituents, and their mass spectra are very different. Therefore, it is difficult to have a unified format for analyzing the spectrum of unknown substances, and it is necessary to use the structural information and knowledge that may be obtained flexibly.

    MS Data Processing and Interpretation

    Software Used to Process and Interpret Mass Spectrometry Data

    • Proteomics software
      • Database search algorithms
      • ProSightPC and ProSightPD

      • De novo sequencing algorithms
      • CycloBranch

      • Homology searching algorithms
      • MS-Homology

    • MS/MS peptide quantification
      • MarkerView Software
      • Mascot Distiller
      • Mascot Server
      • MassChroQ
      • MaxQuant
      • MultiQuant Software
      • OpenMS / TOPP
    • Other software
      • Hiquant
      • TopFD
      • ArtIST by Clover Biosoft¬†
      • ESIprot

    Databases and Resources

    • NIST/EPA/NIH Mass Spectral Library
    • Wiley Registry of Mass Spectral Data, 7th Edition
    • Interpretation of Mass Spectra, 4th Edition
    • The NIST Chemistry WebBook
    • Spectra Online, Galactic

    General Interpretation Steps of Mass Spectrometry

    General Interpretation Steps of Mass Spectrometry

    1. Determine the molecular ion peak from the high-quality end of the mass spectrum, obtain the molecular weight, and preliminarily judge the type of compound and whether it contains Cl, Br, S and other elements.
    2. According to the high resolution data of molecular ion peak, the composition of the compound is given.
    3. The unsaturation of the compound is calculated by the constitutive formula, that is, the number of rings and double bonds in the compound is determined, and the calculation of the unsaturation is helpful to judge the structure of the compound.
    4. High-mass end ion peaks are studied. The ion peak at the high-mass end of mass spectrometry is formed by the loss of fragments of molecular ions. From the fragments lost by molecular ions, it is possible to determine which substituents are contained in the compound.
    5. The low-mass end ion peaks are studied to find the characteristic ion series formed after the fracture of different compounds. For example, the characteristic ion series of n-alkanes are m/z15, 19, 43, 57, 71, etc., and the characteristic ion series of alkylbenzene are m/z91, 77, 65, 39, etc. The type of compound can be inferred from the series of characteristic ions.
    6. Propose the structural unit of the compound through the above-mentioned various aspects of research. According to the molecular weight, molecular formula, sample source, physical and chemical properties of the compound, one or several possible structures are proposed. If necessary, the final result can be obtained based on infrared and nuclear magnetic data.
    7. Verify the results obtained. The verification methods include: decompose the obtained structural formula according to the fragmentation law of the mass spectrum to see if the obtained ion is consistent with the unknown spectrum; check the standard mass spectrum of the compound to see if it is the same as the unknown spectrum; look for the standard sample and make the mass spectrum of the standard sample, and compare with unknown spectra.

    T,C&A Lab

    The processing of MS data has become the task of experts, who can understand the data and its format, as well as software, programs and databases. With the support of the most advanced MS platform and expert team, T,C&A Lab is committed to helping customers with MS experiment design, data collection and interpretation. Welcome to contact our experts for consultation.

    Service Process

    Service Process


    1. Wessels, H. J.; et al. Analysis of 953 human proteins from a mitochondrial HEK293 fraction by complexome profiling. PLoS One 8.7 (2013): e68340.

    Note: this service is for Research Use Only and Not intended for clinical use.

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