Thats a unique idea.You should consider the following idea to enhance your idea so that it would impact uniquely:  present a visual exploration system supporting protein analysis when using gel-free data acquisition methods. The data to be analyzed is obtained by coupling liquid chromatography (LC) with mass spectrometry (MS). LC-MS data have the properties of being nonequidistantly distributed in the time dimension (measured by LC) and being scattered in the mass-to-charge ratio dimension (measured by MS).  describe a hierarchical data representation and visualization method for large LC-MS data. Based on this visualization,  have developed a tool that supports various data analysis steps. Our visual tool provides a global understanding of the data, intuitive detection and classification of experimental errors, and extensions to LC-MS/MS, LC/LC-MS, and LC/LC-MS/MS data analysis. Due to the presence of randomly occurring rare isotopes within the same protein molecule, several intensity peaks may be detected that all refer to the same peptide.  have developed methods to unite such intensity peaks. This deisotoping step is visually documented by our system, such that misclassification can be detected intuitively. For differential protein expression analysis,  compute and visualize the differences in protein amounts beten experiments. In order to compute the differential expression, the experimental data need to be registered. For registration,  perform a nonrigid warping step based on landmarks. The landmarks can be assigned automatically using protein identification methods.  evaluate our methods by comparing protein analysis with and without our interactive visualization-based exploration tool.
['Lars Linsen', 'Julia Löcherbach', 'Matthias Berth', 'Dörte Becher', 'Jörg Bernhardt']
I am writing a research paper on a idea Visual analysis of gel-free proteome data
[{"from": "human", "value": "I am writing a research paper on a idea Visual analysis of gel-free proteome data"}, {"from": "gpt", "value": "Thats a unique idea.You should consider the following idea to enhance your idea so that it would impact uniquely:  present a visual exploration system supporting protein analysis when using gel-free data acquisition methods. The data to be analyzed is obtained by coupling liquid chromatography (LC) with mass spectrometry (MS). LC-MS data have the properties of being nonequidistantly distributed in the time dimension (measured by LC) and being scattered in the mass-to-charge ratio dimension (measured by MS).  describe a hierarchical data representation and visualization method for large LC-MS data. Based on this visualization,  have developed a tool that supports various data analysis steps. Our visual tool provides a global understanding of the data, intuitive detection and classification of experimental errors, and extensions to LC-MS/MS, LC/LC-MS, and LC/LC-MS/MS data analysis. Due to the presence of randomly occurring rare isotopes within the same protein molecule, several intensity peaks may be detected that all refer to the same peptide.  have developed methods to unite such intensity peaks. This deisotoping step is visually documented by our system, such that misclassification can be detected intuitively. For differential protein expression analysis,  compute and visualize the differences in protein amounts beten experiments. In order to compute the differential expression, the experimental data need to be registered. For registration,  perform a nonrigid warping step based on landmarks. The landmarks can be assigned automatically using protein identification methods.  evaluate our methods by comparing protein analysis with and without our interactive visualization-based exploration tool."}]