Is Informed Consent Ever Truly Informed?

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Is informed consent ever truly informed? This is the question posed by Professor Kenneth Boyd, Edinburgh, as he considers the subject in the 40 years of publishing in the Journal of Medical Ethics. Posing more questions than the review itself answers, Boyd surveys the subject in the context of papers published by the journal, showing Read the rest of this article

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What You Need to Know About Food Packaging and the Microbial Environment

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What you wrap your food product in is more than just a handy package for customers to carry around, and it’s more than just branding – food packaging can make or break your food safety measures.  In addition to being a marketing canvas and consumer information billboard, food packaging is often a key player in food safety Read the rest of this article

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Panda Milk, Proteomically

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Griffiths et al. (2015) examined the giant panda (Ailuropoda melanoleuca) milk proteome during lactation, comparing it with two other bear species in addition to other mammals, including humans.1 The researchers were interested in the timing of the changeover from colostrum to mature milk in the panda, since it could reflect the relative immaturity of bear cubs Read the rest of this article

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Biobanking for Studying Rare Disease: ARegPKD and Pediatric Kidney Disease

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One of the major problems faced by clinicians in treating patients with a rare disease is that without the weight of clinical data supporting therapeutic options, clinical management is often based on opinion or anecdotal evidence. Ebner et al. (2015) describe how European clinicians are trying to overcome this critical data shortage for pediatric autosomal Read the rest of this article

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MixGF Handles the Stats on Mixture Spectra Peptide Identifications

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Wang et al. (2014) present an analytical tool, MixGF, which examines the statistics of spectral probabilities for mixture spectra arising from more than one peptide and thus increases identification rates in large-scale proteomics experiments.1 Co-fragmentation of multiple peptide precursors happens frequently in large-scale mass spectrometry-based proteomics experiments, and large-scale studies are becoming the norm in Read the rest of this article

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Affinity Enrichment for Mass Spectrometry-based Interactomics

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Keilhauer et al. (2014) introduced a high-performance affinity enrichment approach for mass spectrometry (AE-MS)- based evaluation of protein-protein interactions.1 The research team contrasted the new methodology with traditional affinity purification (AP-MS), finding that it gave comparable results from a simpler workflow. In order to study the interactome, researchers must focus on the associations between proteins and Read the rest of this article

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HyperLOPIT for the Mouse Stem Cell Proteome

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When researchers want to know more about pluripotency and the push towards stem cell differentiation, they need to know more than just which genes are firing up. Christoforou et al. (2016) suggest that they also need to know what proteins are on the go, and furthermore, where they are spatially located within the cell.1   The researchers propose an upgrade of a technique Read the rest of this article

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Acrylamide and Chips: LC-MS Monitoring Maillard Reaction Products in Starchy Foods

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One of the major by products of the Maillard browning reaction, where reduced sugars interact with the amino acid asparagine under conditions of high heat and low moisture, is acrylamide. The IARC (International Agency for Research on Cancer) classifies this compound, a hydrophilic, polar molecule with low volatility and low molecular weight, as a potential Read the rest of this article

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Clarity in Denoting Mass Spectrometric Peptide Ions

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A recent paper published by Chu et al. (2015) gives an overview of work presented at the Mass Spectrometry and Proteomics Workshop held at the University of Hong Kong in December 2014.1 The paper contains proposals for improving the nomenclature used to describe peptide ions resulting from mass spectrometry analysis. The authors intend that the new Read the rest of this article

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Patients Matter Too: Expanding the Role of Patients as Stakeholders in Biobanking

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In an earlier post, we looked into the role of patients as active participants in biobank setup and management. The papers reviewed showed that, especially for disease-specific biobanks, close collaboration with donors representative of an at-risk population was key to increasing biosample acquisition. Mitchell et al. (2015) review this area further, giving evidence of disease-specific Read the rest of this article

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Plant Antimicrobials and the Food Industry: Part 4 – Application and Regulation

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Antimicrobials derived from plants represent an exciting new direction in food safety and product management for the food industry1. Since consumer preference is for natural products with limited perceived chemical adulteration, replacing traditional food additives with effective plant antimicrobials could win acceptance from buyers. Applications There are three main areas in which plant antimicrobials are Read the rest of this article

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Indigestion Relief with DIGESTIF

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Especially for quantitative label-free proteomics studies, consistency of workflow, methodology and sample preparation in a multi-stage experimental process is key for obtaining meaningful, reproducible data. With bottom-up proteomics, this also includes consistent sample digestion prior to mass spectrometry analysis. Lebert et al. (2014) propose a universal protein standard that monitors this step, providing essential feedback about workflow optimization to researchers.1  Although other methods for monitoring Read the rest of this article

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Proteomics Database Searching with JUMP

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Since identifying peptides from mass spectra is an essential step in mass spectrometry (MS)-based shotgun proteomics, having efficient tools that pull meaningful and valid data out of the raw results is important for researchers. Wang et al. (2014) describe JUMP, a new algorithm developed for searching databases, which they propose as a tool complementary to Read the rest of this article

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Microbial Contamination in Leafy Greens: Open Fields vs Greenhouse Cultivation

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With the current attention on risk factors for foodborne illness, farms are quite rightly under scrutiny for implementing good agricultural practices (GAPs) with regard to minimizing or eradicating contamination during crop production. Holvoet et al. (2014) examined risk factors for microbial contamination in lettuce crops under open field or greenhouse growing systems1. Since fresh leafy Read the rest of this article

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Enabling Proteomics Data Exchange with mzTab

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Proteomics researchers benefit—or suffer, depending on the point of view—from a plethora of file formats with which to store data. Some may be used because of personal preference, while others because of instrument manufacturer specifications. Although all formats store mass spectrometry data, their incompatibility may not allow exchange or comparison between studies. Furthermore, the situation Read the rest of this article

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A Proteomic Ruler That Measures Up

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According to Wiśniewski et al. (2014), using the mass spectrometry (MS) signal generated by histones is a reliable and easily implemented first step in quantitating proteins.1  Furthermore, using the “proteomic ruler” tool developed by the authors, researchers can cut out several steps that potentially introduce error in MS-based proteomic quantitative analysis. Since its introduction into Read the rest of this article

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Measuring Primary Aromatic Amine Migration into Foods by Targeted LC-HRMS

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Sanchis et al. (2015) present a sensitive and efficient method for measuring primary aromatic amine (PAA) contamination in foodstuffs using liquid chromatography coupled with high resolution mass spectrometry (LC-HRMS)1. The method the researchers propose benefits food safety monitoring by providing both targeted measurement of PAAs but also post-target screening for other common migratory contaminants such Read the rest of this article

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Computational Proteomics: At Your Fingertips

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The Journal of Proteomics, official publication of the European Proteomics Association (EuPA), has released a special issue on computational proteomics (2015)1 packed with original research papers on current advances in the proteomics bioinformatics world. Curated by three researchers active within the subject, Paulo Carvalho, Gabriel Padron and Yasset Perez-Riverol, the edition is a valuable resource Read the rest of this article

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Plant Antimicrobials and the Food Industry: Part 3 – Phytochemicals

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Phytochemicals are components within a plant that often impart taste or flavor. Classified as non-nutritive, these factors can also be antimicrobial—a property that has been exploited throughout history. Many cultures use herbs and spices in both cooking and medicine, as much for the pleasant sensations they impart as for their antimicrobial actions against foodborne pathogens, Read the rest of this article

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The E. coli Acetylome: Form and Function

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Castaño-Cerezo et al. (2014) conducted a proteomic evaluation of the Escherichia coli acetylome under four different growth conditions.1 As a post-translational modification (PTM), acetylation of lysine residues contributes to regulation of cellular activity with activation or inactivation of key proteins such as enzymes and other signaling molecules. By modifying nutrition and growth conditions in vitro, the Read the rest of this article

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