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Database retrieval is a complex calculation process, which requires the use of professional mass spectrometry data analysis software for data analysis. The original data from the mass spectrometer was imported into the library search software, and the corresponding analysis parameters were set according to the experimental plan.
The figure shows the distribution of protein coverage. The coverage of most proteins is below 30%. In mass spectrometry methods based on the shotgun (also called bottom-up) strategy, mass spectrometry preferentially scans for more abundant peptides. Therefore, protein coverage is positively correlated with abundance in the sample.
The figure shows the distribution of protein molecular weight. The molecular weights of the identified proteins were present at different stages and were uniformly distributed.
The MaxQuant computational platform for mass spectrometry-based shotgun proteomics-2016-Nature Protocols
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