matlab implemented gui  (MathWorks Inc)

Journal: Methods (San Diego, Calif.)

Article Title: Computer Aided Manual Validation of Mass Spectrometry-based Proteomic Data

doi: 10.1016/j.ymeth.2013.03.004

Figure Lengend Snippet: The Graphical User Interface (GUI) for the MATLAB implementation of CAMV. The left tree contains a searchable list of protein hits in order of decreasing MASCOT score, each peptide assignment made to that protein, and all possible combinations of PTMs for each scan. The middle panel contains the MS2 scan data with pre-labeled peaks. On the right is a survey of the precursor window of the MS1 scan and a view of any quantitation information associated with the assignment. The peptide ladder at the top summarizes the sequencing information: red for an identified fragment, black for missing. A peak color-coding scheme allows for rapid surveillance of the quality of the match: within tolerance (green), within 1.5x tolerance (magenta), unmatched peak (red), and isotopic peak (yellow). Peptides which are pre-emptively excluded by the software appear in red on the left-hand tree. For these peptides, the reason for preemptive exclusion is displayed at the top left of the MS2 panel in place of the sequence ladder, along with an option to proceed with processing.

Article Snippet: Once an analysis has been user- verified, publication-ready figures and spreadsheets containing the appropriate quantitative data can be generated from accepted assignments. fig ft0 fig mode=article f1 fig/graphic|fig/alternatives/graphic mode="anchored" m1 Open in a separate window caption a7 The Graphical User Interface (GUI) for the MATLAB implementation of CAMV.

Techniques: Labeling, Quantitation Assay, Sequencing, Software

Journal: Methods (San Diego, Calif.)

Article Title: Computer Aided Manual Validation of Mass Spectrometry-based Proteomic Data

doi: 10.1016/j.ymeth.2013.03.004

Figure Lengend Snippet: Results of CAMV applied to quantitative tyrosine phosphorylation dataset. (A) All peptide matches following user validation of the dataset. Color code: Agreement between algorithm and user 201/317(green), alternate identification chosen by user 4/317 (yellow), additional assignment included by user 79/317 (blue), and assignment rejected by user 33/317 (red). (B) Distribution of user and CAMV decisions versus MASCOT score. Note that in many cases the user rescued the spectra that were pre-emptively excluded by the software, while in other cases the user rejected the spectral assignment based on the poor quality of the match.

Article Snippet: Once an analysis has been user- verified, publication-ready figures and spreadsheets containing the appropriate quantitative data can be generated from accepted assignments. fig ft0 fig mode=article f1 fig/graphic|fig/alternatives/graphic mode="anchored" m1 Open in a separate window caption a7 The Graphical User Interface (GUI) for the MATLAB implementation of CAMV.

Techniques: Phospho-proteomics, Biomarker Discovery, Software