Recent advances in mass spectrometry (MS)-based proteomics have enabled tremendous
progress in the understanding of cellular mechanisms, disease progression, and the …

Over the past decade, systems biology and plant-omics have increasingly become the main
stream in plant biology research. New developments in mass spectrometry and …

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 …

Glycoproteomics is a powerful yet analytically challenging research tool. Software packages
aiding the interpretation of complex glycopeptide tandem mass spectra have appeared, but …

Elucidating enzyme–substrate relationships in posttranslational modification (PTM) networks
is crucial for understanding signal transduction pathways but is technically difficult because …

Many software tools have been developed for the automated identification of peptides from
tandem mass spectra. The accuracy and sensitivity of the identification software via …

How is protein synthesis initiated locally in neurons? We found that mTOR (mechanistic
target of rapamycin) was activated and then up-regulated in injured axons, owing to local …

The progressive depletion of quiescent “bystander” CD4 T cells, which are nonpermissive to
HIV infection, is a principal driver of the acquired immunodeficiency syndrome (AIDS). These …

The Paragon™ Algorithm, a novel database search engine for the identification of peptides
from tandem mass spectrometry data, is presented. Sequence Temperature Values are …

This manuscript provides a comprehensive review of the peptide and protein identification
process using tandem mass spectrometry (MS/MS) data generated in shotgun proteomic …