SEQUEST
The original database search algorithm, and one of the foundations of modern proteomics. SEQUEST correlates tandem mass spectra of peptides with theoretical spectra derived from protein sequence databases, enabling automated identification of proteins from complex mixtures.
Eng JK, McCormack AL, Yates JR. J Am Soc Mass Spectrom. 1994;5(11):976-989.
ProLuCID
A fast and sensitive SEQUEST-like database search engine developed in the Yates Lab. ProLuCID improves upon SEQUEST with better sensitivity, speed, and support for large-scale database searches including decoy filtering.
Xu T et al. J Proteomics. 2015;129:16-24.
DTASelect
A tool for assembling and filtering protein identifications from shotgun proteomics experiments. DTASelect reassembles peptide information into protein-level identifications with customizable statistical filters.
Tabb DL, McDonald WH, Yates JR. J Proteome Res. 2002;1(1):21-26.
Census
A software tool for quantitative proteomics using stable isotope labeling or label-free strategies. Census supports SILAC, 15N labeling, iTRAQ, TMT, SRM/MRM, and data-independent acquisition experiments from both low- and high-resolution instruments.
Park SK, Venable JD, Xu T, Yates JR. Nat Methods. 2008;5(4):319-322.
MudPIT
Multidimensional Protein Identification Technology (MudPIT) combines strong cation exchange and reverse-phase chromatography in a single biphasic column, enabling deep proteome coverage from complex biological samples without gel-based fractionation.
Washburn MP, Wolters D, Yates JR. Nat Biotechnol. 2001;19(3):242-247.
PINT
A web-based system for storing, visualizing, and querying experimental proteomics data across different conditions and projects. PINT enables systematic comparison of large-scale proteomics datasets.
ProteinClusterQuant
A Java-based software for the analysis of complex proteomics samples using hierarchical clustering and quantitative comparisons. Supports both labeled and label-free experimental designs.
GlycoMSQuant
A Java stand-alone tool for the quantitation of glycosylation sites from mass spectrometry data. Enables site-specific glycan occupancy measurements across experimental conditions.
PCTSEA
Proteomics Cell Type Set Enrichment Analysis that identifies cell type signatures in proteomics datasets by comparing protein expression profiles against curated cell type marker databases.