Kun Zhang

TL;DR: pLink as mentioned in this paper is a software for data analysis of cross-linked proteins coupled with mass-spectrometry analysis, which is compatible with multiple homo- or hetero-bifunctional cross-linkers.

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: Results show that pQuant outperforms Census and MaxQuant in SILAC and (15)N-based quantitation, and estimates the protein ratios and associated CIs by kernel density estimation.

TL;DR: A new algorithm called Alioth, to be integrated into the search engine of pFind, for fast and accurate unrestricted database search on high-resolution MS/MS data, and is comparable to or even faster than the restricted search algorithms tested.

TL;DR: Detailed guidance on running a database search for identification of protein cross‐links using the 2014 version of pLink is provided, which is at least 40 times faster, more versatile, and more user‐friendly.