Liquid chromatography (LC) coupled with data-independent acquisition (DIA) mass
spectrometry (MS) has been increasingly used in quantitative proteomics studies. Here, we …

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 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 …

Calculating the number of confidently identified proteins and estimating false discovery rate
(FDR) is a challenge when analyzing very large proteomic data sets such as entire human …

Percolator is a widely used software tool that increases yield in shotgun proteomics
experiments and assigns reliable statistical confidence measures, such as q values and …

Data-independent acquisition (DIA) is an emerging mass spectrometry (MS)-based
technique for unbiased and reproducible measurement of protein mixtures. DIA tandem …

In common with other omics technologies, mass spectrometry (MS)-based proteomics
produces ever-increasing amounts of raw data, making efficient analysis a principal …

One can interpret fragmentation spectra stemming from peptides in mass-spectrometry-
based proteomics experiments using so-called database search engines. Frequently, one …

In bottom-up discovery proteomics, target–decoy competition (TDC) is the most popular
method for false discovery rate (FDR) control. Despite unquestionable statistical …

Data-independent acquisition (DIA) has revolutionized the field of mass spectrometry (MS)-
based proteomics over the past few years. DIA stands out for its ability to systematically …