Tools

SIMAT
    • SIMAT is a tool for analysis of GC-MS data acquired in SIM mode. The tool provides several functions to import raw GC-SIM-MS data and standard format mass spectral libraries. It also provides guidance for fragment selection before running the targeted experiment in SIM mode by using optimization. This is done by considering overlapping peaks from a library provided by the user. Other functionalities include retention index calibration to improve target identification and plotting EICs of individual peaks in specific runs which can be used for visual assessment.
    • Nezami Ranjbar MR, Di Poto C, Wang Y, and Ressom HW.
      "SIMAT: GC-SIM-MS data analysis tool," BMC Bioinformatics, 2015, 16:259.
      PMID: 26283310
MetaboSearch
    • MetaboSearch is a tool for metabolite identification by searching against four databases: Human Metabolome DataBase (HMDB), Madison Metabolomics Consortium Database (MMCD), METLIN Metabolomics Database, and LIPID Metabolites and Pathways Strategy (LIPID MAPS). The search results from these databases are integrated into a uniformly and non-redundant format based on IUPAC International Chemical Identifier (InChI) key.
    • Zhou B, Wang J, Ressom HW (2012).
      "MetaboSearch: Tool for mass-based metabolite identification using multiple databases."
      PLoS One 7(6): e40096. doi:10.1371/journal.pone.0040096.
      PMID: 22768229

Data & Scripts

Supplementary Page (alignLCMS )
    • Tsai TH, Tadesse MG, Di Poto C, Pannell LK, Mechref Y, Wang Y, Ressom HW (2013).
      "Multi-profile Bayesian alignment model for LC-MS data analysis with integration of internal
      standards.''
      Bioinformatics 29(21):2774-80. PMID: 24013927
Supplementary Page
    • Tuli L, Tsai T-H, Varghese R, Xiao JF, Cheema A, and Ressom HW (2012).
      "Using a spike-in experiment to evaluate analysis of LC-MS data. Proteome Science."
      Proteome Science 10(1):13.
MALDI-TOF glycomics data
    • Ressom HW, Varghese RS, Goldman L, Loffredo CA, Abdel-Hamid M, Kyselova Z, Mechref Y,
      Novotny M, Goldman R (2008).
      "Analysis of MALDI-TOF mass spectrometry data for detection of glycan biomarkers.''
      Pacific Symposium on Biocomputing 13:216-227.
Matlab Scripts & MALDI-TOF proteomics data
    • Ressom HW, Varghese RS, Drake SK, Hortin GL, Abdel-Hamid M, Loffredo CA,
      and Goldman R (2007).
      "Peak selection from MALDI-TOF mass spectra using ant colony optimization.''
      Bioinformatics 23(5):619-626.
MALDI-TOF proteomics data
    • Goldman R, Ressom HW, Abdel-Hamid M, Goldman L, Wang A, Varghese RS, An Y,
      Loffredo CA, Drake SK, Eissa SA, Gouda I, Ezzat S, Seillier-Moiseiwitsch F (2007).
      "Candidate markers for the detection of hepatocellular carcinoma in low molecular weight
      fraction of serum.''
      Carcinogenesis 28(10):2149-53.
Matlab Scripts
    • Ressom HW, Varghese RS, Abdel-Hamid M, Abdel-Latif Eissa S, Saha D, Goldman L,
      Petricoin EF, Conrads TP, Veenstra TD, Loffredo CA, Goldman R (2005).
      "Analysis of mass spectral serum profiles for biomarker selection.''
      Bioinformatics 21(21):4039-4045.