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Sequest Scoring Engine

Known as: Sequest 
A proprietary scoring engine from Thermo Fisher Scientific that can match tandem mass spectra with peptide sequences.
National Institutes of Health

Papers overview

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2010
2010
The effect of interfering ions on search algorithm performance for electron‐transfer dissociation data
Collision‐activated dissociation and electron‐transfer dissociation (ETD) each produce spectra containing unique features. Though… 
2008
2008
SeMoP: a new computational strategy for the unrestricted search for modified peptides using LC-MS/MS data.
A novel computational approach, termed Search for Modified Peptides (SeMoP), for the unrestricted discovery and verification of… 
2008
2008
Automatic validation of phosphopeptide identifications by the MS2/MS3 target-decoy search strategy.
Manual checking is commonly employed to validate the phosphopeptide identifications from database searching of tandem mass… 
2007
2007
N-Glycan structure annotation of glycopeptides using a linearized glycan structure database (GlyDB).
While glycoproteins are abundant in nature, and changes in glycosylation occur in cancer and other diseases, glycoprotein… 
Review
2007
Review
2007
Reliable detection of deamidated peptides from lens crystallin proteins using changes in reversed-phase elution times and parent ion masses.
Identifying deamidated peptides using low-resolution mass spectrometry is difficult because traditional database search programs… 
Highly Cited
2006
Highly Cited
2006
Coupling the immobilized trypsin microreactor of monolithic capillary with muRPLC-MS/MS for shotgun proteome analysis.
A nanoliter trypsin-based monolithic microreactor coupled with muRPLC-MS/MS was reported for shotgun proteome analysis. The… 
Review
2005
Review
2005
Protein Identification Using TurboSEQUEST
SEQUEST is the most widely used software tool for identifying proteins in complex mixtures. It is a mature, robust program that… 
2005
2005
PepSeeker: a database of proteome peptide identifications for investigating fragmentation patterns
Proteome science relies on bioinformatics tools to characterize proteins via their proteolytic peptides which are identified via… 
2005
2005
MASPIC: intensity-based tandem mass spectrometry scoring scheme that improves peptide identification at high confidence.
Algorithmic search engines bridge the gap between large tandem mass spectrometry data sets and the identification of proteins… 
Highly Cited
2003
Highly Cited
2003
Investigative proteomics: Identification of an unknown plant virus from infected plants using mass spectrometry
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