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Applied Biosciences
Pro ID software enables automated protein identification
in complex biological samples when used for analysis of tandem MS data
from proteomics experiments. The software is designed for use on the
API QSTAR Pulsar Hybrid LC/MS/MS system. It incorporates a proprietary
algorithm and can perform error and modification-tolerant searches using
a zone modification feature. It also identifies the particular region
of the peptides in which unexpected modifications are located.
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Bruker Daltonics Proteineer™ Suite
Bruker Daltonics introduces Proteineer DP Digest & Prep station, a
new gel spot digestion robotics workstation for proteomics. The Proteineer
DP Digest & Prep station completes our Proteineer suite, an integrated
comprehensive solution for protein identification and characterization
after 1d- or 2d- gel electrophoresis separation. It complements the previously
introduced Proteineer SP Spot Picker robotics workstation for imaging
of gels, visual analysis, spot selection, and cutting spots out of 2D
gels used for protein separations.
- BIO-RAD
Laboratories ProteomeWorks System
The ProteomeWorks system is an integrated set of tools and technologies
that enables protein function discovery. Innovative new tools for sample
preparation, 2-D electrophoresis, staining, imaging and image analysis,
spot excision, automated protein digestion, mass spectrometry, and bioinformatics
create a seamlessly integrated, high-throughput proteomics platform.
- Genomic
Solutions Investigator Proteomic
System
The Investigator Proteomic System includes 2-D electrophoresis, imaging,
image analysis, automated protein spot excision, protein digestion,
sample preparation for mass spec analysis, data integration, chemicals
and reagents.
- Matrix
Sciences Mascot
Peptide Mass Fingerprint: The experimental data are a list of
peptide mass values from an enzymatic digest of a protein.
Sequence Query: One or more peptide mass values associated with
information such as partial or ambiguous sequence strings, amino acid
composition information, MS/MS fragment ion masses, etc. A super-set
of a sequence tag query.
MS/MS Ion Search: Identification based on raw MS/MS data from
one or more peptides.
- Thermo
Finnigan ProteomeX™ Workstation
The new ProteomeX Workstation enables the rapid set up, execution and
analysis of multidimensional LC/MS methods, providing you with the best
possible technique to characterize your complex proteomics sample.
ProteomeX software creates customized proteomics methods perfect for
protein digests, gel spot analysis, differential expression profiling
and shotgun sequencing of complex samples.
ProteinID: single reversed phase column LC MS/MS.
High Throughput: alternates loading and gradient
elution between two C18 columns for maximum throughput.
Protein Profiling: relative quantitation using Data
Dependent?mass tags and BioWork 3.0's XPRESS to simplify ICAT? experiments.
Multidimensional Protein ID: use 2 dimensions, ion
exchange and reversed phase, to resolve the peptide components of
your most complex samples.
- Thermo
Finnigan SEQUEST (Developed by Yates lab at U.
Wash. (now at Scripps) distributed by Finnigan)
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.
- MDS
Proteomics (Protana) PepSea
PepSea uses the non-redundant EMBL
protein database (nrdb) which currently contains
more than 956,000 entries. The database is updated regularly by C.
Sander's group at EMBL/EBI (European Bioinformatics Institute). (Based
on work of Matthias Mann)
