Development Notes #4: Structure-Assisted Fragment Annotation and Spectrum Validation for LC-MS/MS Quality Control

Part 1 — From Candidate Peptides to Integrated Fragment Annotation Introduction In the previous Development Note, experimentally derived continuous sequence tags were used to reconstruct biologically plausible peptide candidates within the surrounding protein context. Those reconstruc…

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Development Notes #3: Evidence-Driven Peptide Candidate Reconstruction for LC-MS/MS Quality Control — An Algorithm Design Record

Part 1 — Design Philosophy: Why Sequence Tag Search Alone Is Not Enough This article documents the design philosophy and workflow implemented in the current peptide quality-control software. Rather than introducing a general sequence-tag search al…

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