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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 (20) pp.7846-7854.

SpecCons: a java program to generate consensus spectra variants for clustered MS2 spectra

It is widely accepted that consensus MS2 spectra can potentially improve peptide sequencing. Nevertheless there are different ways to generate consensus spectra after MS2 spectra are clustered. To alleviate such problems, this tool (written in Java) is capable of generating multiple consensus variants, depending on user's criteria. Our study has demonstrated that that combining search results over these variants leads to improved accuracy and reliability of De Novo sequencing.
SpecCons.jar - runnable Java program.
User manual- read this first.
Citation: Liu, J; et al. (2010) Improved de novo MS/MS peptide sequencing by subsequent pseudo database search and consensus spectrum variants. to appear at RECOMB Satellite Conference on Computational Proteomics. Manuscript

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.

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