I have a full protein sequence of interest that I want to align against multiple proteins. However, most of these proteins are missing parts because they are Mass Spec data and this tends to happen. Would it be better for me to compare their supposed full protein sequence (the best protein spectra matched full sequence) against the protein of interest or the partial sequence from the mass spec run?
When aligning your protein sequence of interest against multiple proteins, it's generally best to use the full sequence of each protein, even if some parts are missing. This is because the partial sequence from the Mass Spec run may not give you the complete picture of the protein's structure, function, and interactions with other molecules.
Using the full sequence of each protein will allow you to compare the entire protein with your protein of interest, and identify any similarities or differences in their sequences. Additionally, the full sequence can provide important information about protein domains and functional regions that may not be captured by the partial sequence.
However, it's important to keep in mind that the quality of the protein spectra matched full sequence may vary depending on the Mass Spec run and the quality of the data. In cases where the spectra matched full sequence is of low quality, it may be more appropriate to use the partial sequence instead.
In summary, using the full sequence of each protein is generally recommended, but it's important to consider the quality of the data and make a judgement call based on your specific situation.
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