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Enabling
more efficient, accurate proteome analysis
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Sequence Composer
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If this is your first
visit, please read Current Proteomics, 2008, 5, 267-274 (Amino
Acid Sequence Database Suitable for the Protein and Proteome
Analysis.).If you include results from Sequence Composer in a
publication, please cite Current
Proteomics, 2008, 5, 267-274.
We can provide
Demo-version to you.
We value your feedback and suggestions for new features. If
you find any problems, errors, oversights, or just get
unexpected results then please let us know.
Demo-version and feedback.
Contact
US
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What is Sequence Composer? |
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- Database generation
software for improving peptide/protein identification accuracy by
incorporating mature protein structure and diversity into search
algorithms
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- Public protein
databases (such as UNIPROT and NCBI Nr) generally contain the amino acid
sequences of various proteins, but the reality is that protein spectra
obtained from mass spectrometry are based on peptides and proteins
characterized by diversity and mature protein structures. Sequence
Composer uses the annotations appended to each amino
acid sequence to create a database of all possible sequences
incorporating all annotation combinations. Using Sequence Composer
databases improves accuracy of search results when running mass
spectrometry assays.
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Benefits:
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Use
Sequence Composer databases in search algorithms for
peptides/proteins obtained from mass spectrometry to improve
identification scores at low cost
Significantly reduce time and labor
associated with ascertaining validity of potential false
negatives by analyzing amino acid sequence structure
The user-friendly,
graphical UI allows for great flexibility
in database creation according to need
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Feature
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Generates amino acid sequences incorporating
diversity
and mature protein structures Sequence
databases generated incorporate genetic diversity,
transcript
product
diversity, and all possible protein modifications included
in annotations
for each sequence.
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Customizable processing conditions User-selectable processing conditions (shown
below) based on annotations present in downloaded UNIPROT flat files.
VAR_SEQ（Variants from the DNA sequence）
VARIANT（Variants from the alternative splicing events）
CHAIN，PEPTIDE，PROPEP＝Matured Form（Main chain processing）
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Refine search results based on accession and description
②
Users can search and select proteins for processing
based on accession and
description. Feature information is shown for proteins during selection.
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View statistics of post-processing sequences
Users can review the total number of amino acid sequences
generated by the software. (Expansions of statistics functions
planned).
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Processing time in seconds
Only about 47 seconds is required to process the
uniprot_sprot_human.dat file and
generate a complete database. (Using a PC with 1 GB memory)
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☆ Presented as poster at 55th Conference of the American Society for Mass
Spectrometry
☆ Patent pending
☆ Product of joint research with Takao Kawakami of Tokyo Medical University
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Result
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Improving
peptide identification accuracy
The same LCMS/MS results matched with a publically
available database (X axis) and one generated by Sequence
Composer incorporating mature structures and diversity (Y
axis). Low-scoring sequences on the X axis scored higher
on the Y axis.
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Post-processing amino acid sequence
Deleting the signal protein from the sequence causes a
return on the N-terminal peptide, allowing identification
of the alpha chain without relying on the database
annotations. The score also improved through using the
alpha chain sequence alone.
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Maze,Inc.
3-20-2-101
Hatagaya, Shibuya-ku,
Tokyo
151-0072
Tel: +81-3-3378-7430
Contact US
URL: http://www.maze.co.jp/en |
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