Over the last two decades, significant advances in technology and new methodologies have made proteomics an extremely powerful tool for protein scientists, biologists and clinical researchers. Increase in the data produced also creates new challenges for bioinformatics software development.
Whilst automation is not a panacea, it can improve the accuracy of manual tasks as well as freeing up our time for more challenging tasks. The authors explore some particular examples they have come across and lessons learned from them.
Tony Davies and Mohan Cashyap discuss this topic with help from a number of industry experts. Whilst there are undoubted computing and networking issues for regulated industries in allowing working from home as if the user was in the lab, they are not insurmountable.
David is concerned about the “Importance of citing full details of spectral library and search program” in papers. As he points out, “even when the same mass spectrum is searched against two different versions of the NIST/EPA/NIH EI Mass Spectral Library using the same search program, two different compounds can be found as the first Hit”. There are many possible reasons for this, but the version of the spectral library used and the particular search program used make a difference, and should be included in all references.
With a significant proportion of our regular readership probably under home lock-down, we were wondering if we could help you at this difficult time by pointing out some useful online resources. So, when we finally come out of this pandemic, you could do so better skilled and more up-to-date than when we went in to it.
Tony and Lutgarde Buydens give us an update on the planning for the major EuroAnalysis 2021 conference, which is being held in Nijmegen, the Netherlands, at the end of August 2021. At this stage, they are keen to gather suggestions from readers on topics they would like to see covered. Groups are also invited to consider hosting their own event under the EuroAnalysis 2021 banner.
The authors offer many useful points to consider when using pre-processing techniques.
The authors have developed a clever solution to be able to provide constant resolution, high-resolution mass spectrometry data across the full spectrum. In doing so, they have assigned 244,779 unique elemental compositions: a record.
A recent conference on Extractables and Leachables in Hamburg not only allowed two ex-colleagues to meet after many years, but also provided information on developments and trends in the regulatory environment. Not only are ever lower levels of detection required, but also analytical requirements are being placed on companies further back in the materials’ supply chain that have not had to make such considerations before.
Tony Davies and Roy Goodacre raise some issues around the reliance just on vast quantities of data collection in omics experiments. As they put it, should we “just keep throwing the mass spectra, nuclear magnetic resonance data sets and our ion mobility fingerprints onto a big pile for the statisticians to fight over?”.
Hafiz Abdul Azeem recently presented some interesting results from his work on atmospheric aerosols. Following their capture, he combined the optimisation of the extraction process with chromatographic separation and mass spectroscopic detection to identify various sources of pollution through their emission marker fingerprints.1 One spin-off of this work has been the use of a specific biomarker from cellulose combustion to potentially warn of low-heat smouldering in, for example, agricultural materials in bulk storage.
This article provides a valuable summary of the choice of sample clean-up methods available for the quantification of small molecules in body fluids. What are the key factors? Judy outlines the principal processing methods and provides practical advice on protocol development using quantification of serum testosterone in serum samples as the model compound.
Nick Polfer gives an excellent introduction to the recent technique of infrared ion spectroscopy. Ions held in the ion trap of a mass spectrometer can be probed with a tuneable light source, and its photodissociation studied as a function of the photon frequency. Nick believes that the technique will make an impact in small molecule analysis, such as metabolites, drugs and classes of molecules containing many isomers.
Tony Davies continues his quest to find out what you all need to work more efficiently. You will remember that in the last issue, Tony introduced his survey to discover what developments were needed in spectroscopy by readers. Some of the initial responses are explored, and Tony finds that he has opened a “can of worms”.
This article gives a most useful overview of the analysis and sequencing of nucleic acids by matrix-assisted laser desorption/ionisation mass spectrometry, which should interest all readers and may well serve as a useful tutorial article.
Lithium ion batteries power most of the electrical devices we rely on every day. As well as mobile phones, laptops and tablets, they are finding increasing use in vehicles, with electric cars not uncommon on our streets. This article is from a young scientist who has won help for her research through an instrument company’s support programme. You can find out more, read the article and even apply yourself.
The study of metabolites in our sewage systems is not new, but there are particular difficulties with identifying the metabolites from new psychoactive substances, or “legal highs”. The authors describe a wide range of sample collection methodologies and their analysis with mass spectrometry.
Research into climate change takes many directions, but storing carbon or understanding its release from stores is extremely important. Pyrogenic carbon comes from the incomplete burning of biomass, and can be natural, e.g. wild fires, or man-made, e.g. the production of charcoal. The authors describe the uses of a range of spectroscopy techniques to understand the molecular structure of pyrogenic carbon and its role in the global carbon cycle.
The bio theme moves to mass spectrometry in “Solid mixed matrices and their advantages in matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry” by Marek Šebela. Getting the most from various matrices for use in matrix-assisted laser desorption/ionisation (MALDI) has always been a bit of an art, and the introduction of mixed matrices may increase the number of possible combinations but may improve reproducibility and so simplify analysis in the end. The author describes mixed matrices for a range of samples including proteins, peptides, oligosaccharides, oligonucleotides, lipids, polymers and even intact microbial cells!
This article tells us about another: “Fast and versatile ambient surface analysis by plasma-assisted desorption/ionisation mass spectrometry”. They show that surface analysis can greatly benefit from approaches using surface–plasma interactions and that PADI shows significant promise to become a valuable and versatile tool for this.