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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, 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.
In short, SEQUEST performs automated
peptide/protein sequencing via database searching of
MS/MS spectra without the need for any manual sequence
interepretation, though it can make use of interpreted
sequence information if available. |
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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. |
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Quantitative Analysis Tool for both
labeling and labeling free analysis. Visit Census
web page for more info. |
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Quantitative Analysis Tool. Visit RelEx
web page for more info. |
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ProLuCID
is a fast and sensitive tandem mass spectra-based
protein identification program recently developed in the
Yates
laboratory at The Scripps Research Institute.
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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.
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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. |
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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. |
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For truly complex protein
samples, separation prior to mass spectrometry is
increasingly necessary. MudPIT describes the process of
digesting, separating, and identifying the components of
samples consisting of thousands of proteins. Our
protocol uses nanoscale strong cation exchange liquid
chromatography upstream of reversed phase liquid
chromatography online with microelectrospray.
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A modification of the SEQUEST algorithm
allows the software to be run in parallel, sharing the
protein identification task across several computers.
Our Beowulf cluster, Shamu, has processed millions of
spectra to date.
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Research Computing at TSRI has three
SGI
SuperComputers (2x64 CPU and 1x128 CPU, SGI
Origin 2400 and 3800 respectively) and a LINUX Cluster (1584 nodes with 3936 CPU's). run_ms2, PEP_PROBE, ProLuCID and DTASelect2 have been
ported to run on these clusters. Group members can
obtain information on how to use RC computers here.
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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.
[link fixed 6/11/02] |
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NoDupe
identifies similarity among uninterpreted tandem mass
spectra. Optionally, the program can remove duplicate
copies of spectra. |
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QCorr
Add QCorr description here. |
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Charge Prediction Machine: Tool for Inferring Precursor Charge States of Low Resolution Electron Transfer Dissociation Tandem Mass Spectra
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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
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Unitemare is a tool created by Johannes Graumann of CalTech for
migrating existing SEQUEST results to the new unified file format. Unitemare was created
in the Perl programming language.
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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.
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