Yan Fu

TL;DR: The pFind 2.0 software package for peptide and protein identification via tandem mass spectrometry offers a modularized and customized platform for third parties to test and compare their algorithms, and is of high accuracy and high speed.

TL;DR: A novel database-searching software system called pFind (peptide/protein Finder), which employs an effective peptide-scoring algorithm that was reported earlier, is described.

TL;DR: It is shown that higher-energy collisional dissociation (HCD) is of great help to de novo sequencing because it produces high mass accuracy tandem mass spectrometry (MS/MS) spectra without the low-mass cutoff associated with CID in ion trap instruments.

TL;DR: Using pLink-SS, a high-throughput mass spectrometry method, all native disulfide bonds of a monoclonal antibody and ten standard proteins are mapped and many regulatory disulfides involving catalytic or metal-binding cysteine residues are discovered.

TL;DR: A promising approach to utilizing the correlative information for improving the peptide identification accuracy by extending the tandem mass spectral dot product to the kernel SDP (KSDP), which outperforms two SDP-based software tools, SEQUEST and Sonar MS/MS, in terms of identification accuracy.