Untangling the complexities of processing and analysis for untargeted LC-MS data using open-source tools

Untargeted metabolomics is a powerful tool for measuring and understanding complex biological chemistries. However, employment, bioinformatics and downstream analysis of mass spectrometry (MS) data can be daunting for inexperienced users. Numerous open-source and free-to-use data processing and analysis tools exist for various untargeted MS approaches, including liquid chromatography (LC), but choosing the ‘correct’ pipeline isn’t straight-forward. This tutorial, in conjunction with a user-friendly online guide presents a workflow for connecting these tools to process, analyse and annotate various untargeted MS datasets. The workflow is intended to guide exploratory analysis in order to inform decision-making regarding costly and time-consuming downstream targeted MS approaches. We provide practical advice concerning experimental design, organisation of data and downstream analysis, and offer details on sharing and storing valuable MS data for posterity. The workflow is editable and modular, allowing flexibility for updated/changing methodologies and increased clarity and detail as user participation becomes more common. Hence, the authors welcome contributions and improvements to the workflow via the online repository. We believe that this workflow will streamline and condense complex mass-spectrometry approaches into easier, more manageable, analyses thereby generating opportunities for researchers previously discouraged by inaccessible and overly complicated software

Is iconic memory iconic?

Short‐term memory in vision is typically thought to divide into at least two memory stores: a short, fragile, high‐capacity store known as iconic memory, and a longer, durable, capacity‐limited store known as visual working memory (VWM). This paper argues that iconic memory stores icons, i.e., image‐like perceptual representations. The iconicity of iconic memory has significant consequences for understanding consciousness, nonconceptual content, and the perception–cognition border. Steven Gross and Jonathan Flombaum have recently challenged the division between iconic memory and VWM by arguing against the idea of capacity limits in favor of a flexible resource‐based model of short‐term memory. I argue that, while VWM capacity is probably governed by flexible resources rather than a sharp limit, the two memory stores should still be distinguished by their representational formats. Iconic memory stores icons, while VWM stores discursive (i.e., language‐like) representations. I conclude by arguing that this format‐based distinction between memory stores entails that prominent views about consciousness and the perception–cognition border will likely have to be revised