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rIDIMS

Welcome to rIDIMS, an easy-to-use application/package designed to simplify processing direct-infusion mass spectrometry (DIMS) data. Spectra obtained by DIMS can be challenging. There may be few samples and/or samples with limited surface area. In these cases, the chronogram presents challenging curves for processing. Many existing algorithms are not prepared to process regions with zeroed scans, for example. rIDIMS emerges as the ideal tool for processing DIMS data with an innovation in reproducible and statistically robust scan selection. See a typical example of a chronogram below.

TICs_example
TICs_example

This example is from a single sample. In this single run (injection) there are TICs with valid and invalid scans (regions with zeroed scans and noise). The goal is to extract valid scans from this spectrum in a rational and reproducible manner. To do this, the rIDIMS algorithm removes regions with zeroed scans and noise, and then selects TICs that present values above an established threshold (that contains valid scans). Therefore, in a chronogram there are several scans of the same sample that can be combined into consensus spectra. * For cases where there is only one sample that can be analyzed and the analyst wants to obtain scans in representative sets of that sample, the analyst can choose to create in-silico replicas. Since these are valid scans of the same sample, we suggest an innovation: the creation of in-silico replicas. That is: selection of valid scans and grouping of these scans into 3 groups to form a triplicate. More details about this innovation can be found in our publication: <>. Where we show how to form these sets in a way that they do not present statistical differences between them.

rIDIMS should be installed with the pak package. pak is the best option because it is able to install automatically all dependencies from various sources such as CRAN, Bioconductor, GitHub, URLs, git repositories.

  1. Install pak package
  1. Install rIDIMS package
pak::pkg_install("url::https://github.com/BioinovarLab/rIDIMS/releases/download/v0.6.5/rIDIMS_0.6.5.tar.gz")

Start the application

Screenshot

Prerequisites:

  • Windows: Install the latest version of Rtools. It is advised to install in the default location which is C:.
  • Linux: Make sure to have r-base-dev installed. HowTO.
  • OSX: Make sure to have Xcode developer tools from Apple installed. Tutorial.

Click here for the extended tutorial.