Bioinformatics Analysis FAQ Summary
• Can you provide a detailed installation and usage tutorial for the Proteome Discoverer software?
Proteome Discoverer is a professional software launched by Thermo Fisher Scientific for mass spectrometry data analysis, widely used in proteomics research, especially in quantitative analysis, protein identification, and post-processing analysis. Below is a detailed installation and usage tutorial.
• Where can I see the different interaction modes between proteins in STRING?
In the STRING database, the different interaction modes between proteins can be viewed through the 'Protein-Protein Interaction (PPI) Network' view. Users can enter the names of proteins of interest to see related interaction types, such as experimentally verified interactions, predicted interactions, and co-expression relationships, among others. STRING provides various filters to help users select different types of interactions and view detailed information about the proteins, functional annotations, and pathways involved. Through this platform, users can also download data for further analysis.
In the results of non-targeted metabolomics, when there are many differential metabolites that meet the screening criteria VIP > 1 and P < 0.05, the following steps can be taken to select metabolites with biological significance:
• How to predict potential antigen epitopes of proteins with known sequences but unknown structures?
To predict the antigen epitopes of proteins with known sequences but unknown structures, sequence-based prediction methods (such as BepiPred, NetMHC, etc.) and structure-based prediction methods (such as SWISS-MODEL, Phyre2, and other homology modeling tools) can be used. Tools that combine sequence and structural information (such as IEDB) further enhance prediction accuracy. Ultimately, experimental validation of the predictions through ELISA, Co-IP, and other methods is necessary to ensure the accuracy of the epitopes.
Mass spectrometry (MS) can be used to detect the content of a certain sample (such as proteins, lipids, metabolites, etc.) in animal tissues. The advantages of mass spectrometry include its high sensitivity, high selectivity, and the ability to simultaneously detect multiple components in complex samples. When using mass spectrometry to analyze animal tissue samples, appropriate preprocessing of the tissues is required to extract the target molecules and remove impurities that may interfere with the analysis.
• Why does the baseline of HPLC samples become unstable during injection?
The instability of the baseline during HPLC sample injection can be caused by multiple factors, with common reasons including sample contamination, uneven mobile phase, leaks in the injection system, temperature fluctuations, pump system instability, and detector malfunctions. Solutions include filtering or centrifuging the samples, ensuring the quality and degassing of the mobile phase, checking the injection system and seals, ensuring temperature control stability, regular maintenance of the pump, and calibrating the detector. A comprehensive check of these factors can help identify and resolve the issue of baseline instability.
• What are the operating steps of MALDI-TOF MS?
MALDI-TOF MS (Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry) is a method commonly used for the analysis of biological samples, typically including the following key operational steps: sample preparation, sample introduction into the instrument, laser desorption ionization, ion acceleration and flight, mass spectrometry detection, and data analysis.
In biological research, a biplot is a graphical statistical analysis method commonly used in Principal Component Analysis (PCA) and Multivariate Analysis of Variance (MANOVA). This method can simultaneously represent samples and variables on a two-dimensional plane, clearly illustrating the relationships between samples and variables. Here are the detailed steps for analyzing a biplot:
While standards are not essential in DLS analysis, they help improve the accuracy and reliability of the analysis in terms of experimental calibration and data comparison.
The requirements for cell quantity in the detection of disulfide bonds and free cysteine in biopharmaceuticals depend on several factors, including the sensitivity of the analytical method, the expression level of the target protein, and the desired detection accuracy.
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