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SIMS - Sequential Interval Motif Search
SIMS (Sequential Interval Motif Search) is a software tool design to perform unrestrictive PTM search over tandem mass spectra. In other words, users do not have to characterize the potential PTMs. Instead, users only need to specify the range of modification mass for each individual amino acid. Interally SIMS uses a database search algorithm, thus it requires a protein sequence database in fasta format and a mass spectrum as input.
Available Binary (for Windows XP and Linux Red Hat) - SIMS_binary.zip
Available Source Code (for Windows XP and Linux Red Hat) - SIMS_sources.zip
Citation: Liu, J; et al. (2008) Sequential Interval Motif Search: Unrestricted Database Surveys of Global MS/MS Data Sets for Detection
of Putative Post-Translational Modifications. Anal. Chem.
ySelect and yRatios
ySelect.c (with documentation) - Select MS/MS spectra according to their Statquest confidence level.
yRatios.c (with documentation) - Quantitative profiling through 18O labeling and MS/MS spectra analysis.
Web Tools Available for Public
EcoliSpec - E.COLI CLUSTER INTERPRETER TOOL
HumanSpec - HUMAN CLUSTER INTERPRETER TOOL
MouseSpec - MOUSE CLUSTER INTERPRETER TOOL
YeastSpec - YEAST CLUSTER INTERPRETER TOOL
Public Accessible Database from EmiliLab
Yeast Interacteome Project - Global landscape of protein complexes in the yeast Saccharomyces cerevisiae
Mouse Proteome Project - Global mass spectrometry analysis of Mouse Proteome
C2C12 - C2C12 Dataset
Emililab Software
Published Software - Includes MCATSCAN, Twinpeaks and Proteogest
Publication Documents
Supp. Table 8 For Hu et al - Table 8 from Hu et al. paper
Supp. Table 9
For Hu et al - Table 9 from Hu et al. paper
