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How do shotgun proteomics algorithms identify proteins?

Instrumentation aside, algorithms for matching mass spectra to proteins are at the heart of shotgun proteomics. How do these algorithms work, what can we expect of them and why is it so difficult to find protein modifications?

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Figure 1: Shotgun proteomics identifies proteins from the fragmentation mass spectra of their constituent peptides.


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Marcotte, E. How do shotgun proteomics algorithms identify proteins?. Nat Biotechnol 25, 755–757 (2007).

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