We describe pLink 2, a search engine with higher speed and reliability for proteome-scale
identification of cross-linked peptides. With a two-stage open search strategy facilitated by …

We have developed pLink, software for data analysis of cross-linked proteins coupled with
mass-spectrometry analysis. pLink reliably estimates false discovery rate in cross-link …

This paper describes the pFind 2.0 software package for peptide and protein identification via
tandem mass spectrometry. Firstly, the most important feature of pFind 2.0 is that it offers a …

In tandem mass spectrometry (MS/MS)-based proteomics, search engines rely on comparison
between an experimental MS/MS spectrum and the theoretical spectra of the candidate …

We present a sequence-tag-based search engine, Open-pFind, to identify peptides in an
ultra-large search space that includes coeluting peptides, unexpected modifications and …

De novo peptide sequencing has improved remarkably in the past decade as a result of
better instruments and computational algorithms. However, de novo sequencing can correctly …

Great advances have been made in mass spectrometric data interpretation for intact
glycopeptide analysis. However, accurate identification of intact glycopeptides and modified …

The precise and large-scale identification of intact glycopeptides is a critical step in glycoproteomics.
Owing to the complexity of glycosylation, the current overall throughput, data quality …

We developed a high-throughput mass spectrometry method, pLink-SS ( http://pfind.ict.ac.cn/software/pLink/2014/pLink-SS.html
), for precise identification of disulfide-linked peptides. …

10.7554/eLife.12509.001 To improve chemical cross-linking of proteins coupled with mass
spectrometry (CXMS), we developed a lysine-targeted enrichable cross-linker containing a …