Search Software

  • CD-HIT is a program for clustering large protein database at high sequence identity threshold. The program removes redundant sequences and generate a database of only the representatives.

  • Bruker Daltonics ClinProTools system is an integrated set of tools for biomarker discovery and clinical proteomics search.

  • InterProScan software combines several protein motifs/domains search tools together.
  • Mascot is a mass spectral search algorithm that uses mass spectrometry data to identify proteins from primary sequence databases.

  • MZmine 2 is an open-source project delivering a software for mass-spectrometry data processing, with the main focus on LC-MS data.

  • ProteinPilot™ Software can perform protein identification and quantitation, along with prediction of hundreds of peptide modifications and non-tryptic cleavages simultaneously.

  • The ProteoWizard Library and Tools are a set of modular and extensible open-source, cross-platform tools and software libraries that facilitate proteomics data analysis.

  • Scaffold is a computer program that integrates search results from search algorithms such as Sequest, X!tandem ,Mascot, Phenyx, OMSSA and Spectrum Mill to generate peptide identification and protein identification probabilities.

  • TINT is a data management and analysis tool for proteomics.  It can be used to run batch jobs of Sequest and Scaffold. 

    TINT can be accessed here:

  • X! Tandem is open source software that can match tandem mass spectra with peptide sequences. X! tandem generates theoretical spectra for peptide sequences using information about intensity associated with amino acids.