The Trans‐Proteomic Pipeline (TPP) is a suite of software tools for the analysis of MS/MS
data sets. The tools encompass most of the steps in a proteomic data analysis workflow in a …

The analysis of the large amount of data generated in mass spectrometry–based proteomics
experiments represents a significant challenge and is currently a bottleneck in many …

Proteogenomics is an area of research at the interface of proteomics and genomics. In this
approach, customized protein sequence databases generated using genomic and …

A statistical model is presented for computing probabilities that proteins are present in a
sample on the basis of peptides assigned to tandem mass (MS/MS) spectra acquired from a …

We present a statistical model to estimate the accuracy of peptide assignments to tandem
mass (MS/MS) spectra made by database search applications such as SEQUEST. Employing …

Affinity purification coupled with mass spectrometry (AP-MS) is a widely used approach for
the identification of protein-protein interactions. However, for any given protein of interest, …

The shotgun proteomic strategy based on digesting proteins into peptides and sequencing
them using tandem mass spectrometry and automated database searching has become the …

Circular RNAs (circRNAs) are an intriguing class of RNA due to their covalently closed structure,
high stability, and implicated roles in gene regulation. Here, we used an exome capture …

There is a need to better understand and handle the 'dark matter' of proteomics—the vast
diversity of post-translational and chemical modifications that are unaccounted in a typical …

The completion of the sequencing of the human genome and the concurrent, rapid
development of high-throughput proteomic methods have resulted in an increasing need for …