Biomedical Technology Resources
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Yeast Resource Center

Trisha N. Davis, Ph.D.
P41GM103533
Active

Center Overview

The Yeast Resource Center (YRC) is a NCRR and NIGMS Biomedical Technology Research Center based at the University of Washington in Seattle, Washington. The YRC's mission is to (1) exploit the budding yeast Saccharomyces cerevisiae to develop novel technologies for investigating and characterizing protein function and protein structure (2) facilitate research and extension of new technologies through collaboration, and (3) actively disseminate data and technology to the research community.

Through collaboration, the YRC freely provides resources and expertise in six core technology areas:

  1. Protein Tandem Mass Spectrometry
    Tandem mass spectrometry is a powerful technique for characterizing a proteome. The YRC is using mass spectrometry to study the structure and composition of protein complexes, sites and mechanisms of post-translational modifications, protein regulation, and protein quantification. (Led by John Yates and Michael MacCoss)
  2. Protein Sequence-Function Relationships
    Understanding the functional properties of proteins is of paramount importance. The YRC has developed a method that uses protein display technology in conjunction with high-throughput sequencing to enable high-resolution mapping of protein sequence-function relationships and the analysis of protein function on a massive scale. (Led by Stan Fields)
  3. Quantitative Phenotyping
    The YRC develops sequencing and competitive growth technologies to study the functional consequences of protein variation in yeast and humans. (Led by Maitreya Dunham)
  4. Protein Structure Prediction and Design
    The YRC applies data describing intra and intermolecular interactions with the Rosetta computer program to better predict and design macromolecular structures and interactions. (Led by David Baker)
  5. Fluorescence Microscopy
    The YRC develops technologies based on live-cell microscopy and FRET to map the relative position of proteins within large multi-protein complexes in living cells. (Led by Trisha Davis and Eric Muller)
  6. Computational Biology
    The YRC develops and applies computational techniques to model and understand protein structure and function. This research emphasizes statistical and machine learning techniques, such as hidden Markov models and support vector machines. (Led by William Noble)

A current list of YRC publications may be found here. The volume and breadth of publications illustrate the impact of the YRC on technology development and collaborative research in a broad range of research areas.

Resources

ResourceDescriptionSupported PlatformsSupported FormatsData TypeData Size (compressed)
BiblioSpec
Yeast Resource Center
NIGMS

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.

Linux, Windows N/A N/A
Bullseye
Yeast Resource Center
NIGMS

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.

Linux N/A N/A
Census
Yeast Resource Center
NIGMS

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

Linux, Mac OSX, Windows N/A N/A
Charge Prediction Machine (CPM)
Yeast Resource Center
NIGMS

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

N/A N/A
Crux
Yeast Resource Center
NIGMS

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

Linux FASTA, MS2, SQT, Text...(more) N/A N/A
DFCalc
Yeast Resource Center
NIGMS

Biological mass spectrometry need not be limited to peptides, of course. DFCalc is software designed to assist the interpretation of tandem mass spectra from DNA molecules. The program predicts the fragment ions for known sequences, producing a list to be compared against a spectrum.

N/A N/A
DTASelect/Contrast
Yeast Resource Center
NIGMS

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.

Linux, Mac OSX, Windows MS2, SQT N/A N/A
FRETSCAL
Yeast Resource Center
NIGMS

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.

Matlab N/A N/A
GutenTag
Yeast Resource Center
NIGMS

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.

N/A N/A
Hardklor
Yeast Resource Center
NIGMS

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.

N/A N/A
IDCalc
Yeast Resource Center
NIGMS

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

Windows N/A N/A
Lorikeet
Yeast Resource Center
NIGMS

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. Lorikeet uses the Flot plotting library.

Web-Based N/A N/A
MakeMS2
Yeast Resource Center
NIGMS

A windows client program used to produce compact and easily parsed text based file formats for shotgun proteomic spectra and indentifications.

Windows N/A N/A
MScout
Yeast Resource Center
NIGMS

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

Linux N/A N/A
Mzxml2msn
Yeast Resource Center
NIGMS

Mzxml2msn is a Java program we developed to convert mzXML to ms1 and ms2 files. Although our ProLuCID and Census can handle mzXML files, we prefer to use ms2 and ms1 files for computational effeciency.

Linux, Mac OSX, Windows N/A N/A
Nodupe
Yeast Resource Center
NIGMS

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

N/A N/A
PAnDA
Yeast Resource Center
NIGMS

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.

N/A N/A
PatternLab
Yeast Resource Center
NIGMS

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.

Windows N/A N/A
Percolator
Yeast Resource Center
NIGMS

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.

Linux, Windows N/A N/A
Philius
Yeast Resource Center
NIGMS

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

Linux N/A N/A
ProLuCID
Yeast Resource Center
NIGMS

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

N/A N/A
QCorr
Yeast Resource Center
NIGMS

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

N/A N/A
qvality
Yeast Resource Center
NIGMS

qvality performs nonparametric estimation of posterior error probabilities.

N/A N/A
RawExtractor
Yeast Resource Center
NIGMS

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.

N/A N/A
RelEx
Yeast Resource Center
NIGMS

Quantitative Analysis Tool. Visit RelEx web page for more info.

N/A N/A
Rosetta
Yeast Resource Center
NIGMS

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.

N/A N/A
SEQUEST
Yeast Resource Center
NIGMS

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 initally identifies amino acid sequences in the database that match the measured mass of the peptide,...

Linux N/A N/A
SkyLine
Yeast Resource Center
NIGMS

An advanced windows program for building methods and analyzing data from SRM/MRM targeted proteomics experiments. New release of v0.5 and several videos demonstrating the capabilities and how to use the software.

Windows N/A N/A
Topograph
Yeast Resource Center
NIGMS

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.

Windows N/A N/A
YADA
Yeast Resource Center
NIGMS

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.

N/A N/A
YRC Public Data Repository
Yeast Resource Center
NIGMS

Provides access to scientific experimental data resulting from collaborations and technology development involving the YRC. The data has been made public either through publication or by specific consent of the researchers involved. Data include yeast two-hybrid, tandem mass spectrometry, protein complex prediction, and fluorescence microscopy.

Fluorescent Stained Microscopy N/A
YRC Public Image Repository
Yeast Resource Center
NIGMS

A very large database and accompanying web application containing fluorescent microscopy images depicting the localization, co-localization and FRET (fluorescence energy transfer) of proteins in cells--particularly in the budding yeast Saccharomyces cerevisiae.

Fluorescent Stained Microscopy N/A