Outline of SMIRFE Manuscripts


SMIRFE Algorithm Manuscript

  • Purpose: describe the algorithm sufficiently for publication
  • Target Journal: ACS (maybe analytical chemistry)

Figures and Tables

  • SMIRFE Overview Flowchart
  • Relative NAP equations.
  • Scoring equations.
  • Figure of clique and superclique representation.
  • Table describing samples and spectra properties analyzed.
  • The replicate two spectra of the ECF-treated amino acid standards.
  • Table of assignment results.
  • Graph of SMIRFE database size based on m/z range.
  • Graph of search results size based on m/z.
  • Graph of assignment ambiguity vs m/z.
  • Scatterplot of m/z deviation vs m/z.

Classification of molecules based on molecular formula

  • Purpose: describes the creation of RF classifiers that classify EMFs into lipid classes.
    • Also describes different ways to cross-validate SMIRFE results.
  • Target Journal: Metabolomics

Figures and Tables

  • Overview of the RF classifier building
  • Description of lipid classifier hierarchy
  • Truth table results for classification of each lipid class based on database (LIPIDMAPS).
  • Table describing samples and spectra properties analyzed (P01 dataset).
  • Example spectra (100Cpos and 100Npos).
  • Graph showing m/z limitations of the lipid databases and their effects on classifier building.
  • Theoretical lipid class histograms by m/z.
  • Table of classification statistics on the P01 dataset.

Clinical Implications of differential lipid expression in NSCLC

  • Purpose: presents clinical relevance of differential lipid expression between cancer and non-cancer.
  • Target Journal: cancer field, AACR journal (high impact).

Figures and Tables

  • Table describing samples and spectra of the P01 dataset.
  • Example spectra (100Cpos and 100Npos).
  • Observed lipid Class histogram vs m/z.
  • Table of all significant fold-change spectral features with presumed IMF (EMF) (put in supplemental).
  • Fold Change labeled by lipid class vs m/z.
  • Mevalonate pathway figure with presumed sites of drug action.

Possible additional analyses

  • Analyze Truvian insurance record dataset to see if there is a lower incidence/prevalence of lung cancer for people on statins.

M/Z Correction of Global Shift and Ion Repulsion

  • Purpose: describes an approach enabled by SMIRFE and cross-validation.
  • Target Journal: ACS (maybe).

Figures and Tables

  • Table describing samples and spectra properties analyzed.
  • Example spectra.
  • Offset m/z deviation vs m/z.
  • Offset m/z deviation vs ion repulsion.
  • Equations for repulsion correction.
  • New scoring equation that includes m/z comparisons.
  • Graph of search results size based on m/z.
  • Graph of assignment ambiguity vs m/z.

-- JoshuaMitchell - 17 Sep 2018
Topic revision: r1 - 17 Sep 2018, JoshuaMitchell
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