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YRC Software

A major component of technology development in the YRC has been development of software used to model, analyze, and visualize data. Below is a list of software developed by, or in partnership with, the YRC.

Quantitative Proteomics


Quantitative Analysis Tool for both labeling and labeling free analysis. Visit Census web page for more info.


Skyline is a freely-available and open source Windows client application for building Selected Reaction Monitoring (SRM) / Multiple Reaction Monitoring (MRM), Parallel Reaction Monitoring (PRM – Targeted MS/MS), Data Independent Acquisition (DIA/SWATH) and targeted DDA with MS1 quantitative methods and analyzing the resulting mass spectrometer data. It aims to employ cutting-edge technologies for creating and iteratively refining targeted methods for large-scale quantitative mass spectrometry studies in life sciences.

Protein Cross-linking Mass Spectrometry

Crux (search-for-xlinks)

Crux analyzes shotgun proteomics tandem mass spectra, associating peptides with observed spectra.


Free, open-source application for identification of cross-linked peptides from mass spectra.


ProXL is a web application and database for the visualization, analysis, and sharing of protein cross-linking mass spectrometry results.

Mass Spectrometry Proteomics


A suite of software tools for creating and searching MS/MS peptide spectrum libraries. The software is particularly useful for those performing repeated proteomics profiling experiments on the same organism. After the identity of a peptide spectrum has been determined, this information can be used to speed and improve all future analyses.


Bullseye takes high resolution accurate masses from full scan spectra and matches these masses to tandem MS scan events. The MS/MS spectra can then be database searched with a narrow precursor ion mass to reduce database search space and improve peptide sequence identification.

Charge Prediction Machine (CPM)

Charge Prediction Machine: Tool for Inferring Precursor Charge States of Low Resolution.


Chorus is a cloud-based platform for proteomics data management, processing, and analysis. It incorporates several tools developed by the YRC.


Crux analyzes shotgun proteomics tandem mass spectra, associating peptides with observed spectra.

DTASelect / Contrast

DTASelect and Contrast were designed to make interpretation and comparison of proteomic data faster and more effective. DTASelect organizes and filters SEQUEST identifications, reducing the time required to interpret the results for each sample. Contrast differentiates multiple samples and comprises a powerful meta-analytical tool.


GutenTag is software to identify peptides by the sequence tagging technique. SEQUEST searches a sequence database by mass, but GutenTag searches with short sequences derived directly from the spectrum.


A computer program for the analysis of high resolution mass spectrometry data. Hardklor will return monoisotopic m/z and charge states for single or overlapping peptide/protein isotope distributions.


An implementation of the method reported by Kubinyi, Analytica Chimica Acta, 247 (1991) 107-119 for the prediction of isotope distributions.


MScout is a program that we have used for assessing LC-MS data quality.


Lorikeet is a JQuery plugin to view MS/MS spectra annotated with fragment ions. The viewer is interactive with zoom capabilities, selection of fragment types, switching annotations on and off etc. The plugin can, optionally, also render a MS1 spectrum below the MS/MS spectrum.


A relational database and accompanying web application for unifying, storing, viewing, and comparing protein mass spectrometry results from a wide range of proteomics platforms.


Mzxml2msn is a Java program developed by the Yates lab to convert mzXML to ms1 and ms2 files.


NoDupe identifies similarity among uninterpreted tandem mass spectra. Optionally, the program can remove duplicate copies of spectra.


An acronym for Post Analysis Data Acquisition. PAnDA uses the Hardklor feature finder to define the molecular species in an LC-MS analysis and then uses this information to automatically construct new methods to specifically target features that were missed in subsequent analyses. PAnDA is particularly powerful when running technical and biological replicates to increase the fraction of the features that can be assigned a peptide identity.


Provides tools for analyzing shotgun proteomic data quantitated by spectral counting (with DTASelect) or labeling (with Census). The modules provide means to point differentialy expressed proteins / peptides (ACFold / TFold modules), find proteins with simmilar expression profiles in time-course experiments (TrendQuest module), find unique proteins to a state (Area proportional venn diagram module) and help interpreting results according to the Gene Ontology (Gene Ontology Explorer module). Minimum requirements: a computer with Windows XP SP2.


A semi-supervised machine learning approach for improving the analysis of tandem mass spectrometry data of peptides. Percolator uses a machine learning technique call a support vector machine to dynamically discriminate between correct and decoy spectrum identifications obtained by database searching. By using our approach, we are able to identify approximately 50% more peptides from a given μLC-MS/MS dataset.


ProLuCID is a fast and sensitive tandem mass spectra-based protein identification program recently developed in the Yates laboratory at The Scripps Research Institute.


The YRC contributes to the ProteoWizard project, which is a set of modular and extensible open-source, cross-platform tools and software libraries that facilitate proteomics data analysis.


The QCorr algorithm compares a tandem mass spectrum to a reversed copy of the same spectrum using a cross correlation.


RawExtractor is a program to extract MS and MS/MS spectra from RAW files generated by Thermo mass spectrometers, such as LTQ, LTQ-Orbitrap, LCQ, and stores the spectra in ms1, ms2 or mzXML file format. The spectra files generated by RawExtractor program are used as input for protein identification programs SEQUEST, ProLuCID and quantitatation program Census.


A method for performing protein identification & peptide sequencing by utilizing mass spectrometry fragmentation patterns to search protein and nucleotide databases has been developed by our lab. Our program, SEQUEST, converts the character-based representation of amino acid sequences in a protein database to fragmentation patterns which are compared against the MS/MS spectrum generated on the target peptide. The algorithm initially identifies amino acid sequences in the database that match the measured mass of the peptide, compares fragment ions against the MS/MS spectrum, and generates a preliminary score for each amino acid sequence. A cross correlation analysis is then performed on the top 500 preliminary scoring peptides by correlating theoretical, reconstructed spectra against the experimental spectrum. Output results are displayed accordingly.


Topograph is an advanced program for the analysis of proteomics data using stable isotope labeling. This software is still in the early stages of development. Improvements are added regularly.


YADA can deisotope and decharge high-resolution mass spectra from large peptide molecules, link the precursor monoisotopic peak information to the corresponding tandem mass spectrum, and account for different co-fragmenting ion species (multiplexed spectra). YADA also enables a pipeline consisting of ProLuCID and DTASelect for analyzing large-scale middle-down proteomics data.

Protein Structure Prediction


Philius uses Hidden Markov Models (HMM) to predict transmembrane protein topology and signal peptide position.


Rosetta is a molecular modeling software package for understanding protein structures, protein design, protein docking, protein-DNA and protein-protein interactions. The Rosetta software contains multiple functional modules, including Rosetta ab initio, RosettaNMR, RosettaDesign, RosettaDock, Rosetta Fragment Selection, Rosetta Nucleic Acids, RosettaLigand, and more.



JobCenter is a novel client/server architecture for distributing and executing computing jobs across heterogeneous computing environments, such as those typically found in research laboratories.


Mason is a portable web site module designed to visualize and compare annotated features of one or more nucleotide or protein sequence.


A relational database and accompanying web application for unifying, storing, viewing, and comparing protein mass spectrometry results from a wide range of proteomics platforms.


ProXL is a web application and database for the visualization, analysis, and sharing of protein cross-linking mass spectrometry results.


SnipViz is a client-side software tool designed to disseminate multiple versions of related gene and protein sequences on web sites.

Computational Biology


qvality performs nonparametric estimation of posterior error probabilities.

Fluorescence Microscopy


FRETSCAL screens images of cells that contain CFP and YFP tagged proteins in order to determine the extent of energy transfer(FRET)between the two fluorophores. The graphical user interface (GUI) of FRETSCAL allows the user to specify criteria that are used to identify areas of interest (AOIs) in the images.