Analytical science advances最新文献

Hydrophobic interaction chromatography (HIC) is a chromatographic technique that mainly targets the separation of biomolecules (intact proteins, monoclonal antibodies, etc.) based on the difference in surface hydrophobicity while applying non-denaturing conditions. This protocol paper provides guidelines for setting-up robust HIC analysis and considers the instrument configuration, mobile-phase and sample preparation, as well as chromatographic conditions and settings. The separation of a mixture of intact proteins and monoclonal antibodies is demonstrated by applying conventional HIC conditions, that is, using a mildly hydrophobic (C₄) stationary phase in combination with an inverse ammonium sulphate gradient dissolved in aqueous phosphate buffer. The effect of sample-preparation conditions on sample breakthroughs is presented. Finally, good run-to-run repeatability (relative standard deviation < 2%) is demonstrated for five different columns obtained from three different column lots, considering chromatographic retention, peak width, peak area and column pressure.

Analytical sciences are among the most dynamically developing fields and have been inherently integrated into many various scientific disciplines. At the same time, Early Career Researchers are among those whose contribution to this dynamic growth cannot be simply overestimated. Hence, in this special issue ‘From one Early Career Researcher to the next’, we are presenting a series of editorials with Q&A from five emerging scientists of different analytical fields, including omics, environmental and data sciences. Importantly, all our guests boast not only scientific excellence and high-quality research but also the substantial international experience gained during their Ph.D. or postdoctoral training. For this editorial, we are presenting Dr. Mateusz Krzysztof Łącki.

Dr. Mateusz Krzysztof Łącki comes from Warsaw in Poland, where he studied economics at the Warsaw School of Economics, and mathematics at the University of Warsaw (and preferred the latter). After getting master's titles in both fields, he joined the bioinformatics group of Prof. Anna Gambin at the University of Warsaw. There, he completed his Ph.D. in computer science, after which he was awarded the best Ph.D. in bioinformatics prize by the Polish Bioinformatics Society. After that, together with his dear wife, he moved to Mainz and started working at Prof. Tenzer's mass spec core facility at the Johannes Gutenberg University Medical Center.

I have a Ph.D. in computer science and both a master's and bachelor's titles in mathematics and computational economics. During the Ph.D., I was introduced to the field of mass spectrometry and collaborated extensively with top–down mass spectrometrists: prof. Frank Sobott, prof. Dirk Valkenborg and Dr. Frederik Lermyte. Back then, we were trying to address problems with a relative lack of software for the analysis of top–down mass spectrometry data in proteomics. In that emerging technique, proteins are fragmented directly in the mass spectrometer instead of being digested by trypsin before being introduced into the instrument. Whole proteins are much larger than peptides, can obtain many more charges during the ionization phase, and their fragmentation in the instrument provides much more observable fragments. Solving this problem basically required writing a whole peptide-centric analytical pipeline from scratch.

I am currently helping in the optimization of the construction of the data collection on a timsTOF device. timsTOF mass spectrometers are relatively new instruments used in exploratory proteomics that pair traditional liquid chromatography and mass time-of-flight mass spectrometry with ion mobility separation. Why is that advantageous? The biggest problem with applying mass spectrometry in biology is the overall complexity of the sample. This creates a technical problem, as the detector can get overwhelmed by the sheer number of ions. This also creates a data interpretation problem. To overcome these problem

Close to the end of their PhD many young researchers are confronted with the question of whether to apply for a postdoctoral position or directly for jobs in industry. While starting a career in industry shortly after finishing a PhD degree can help to achieve high-ranking positions earlier, extending the academic education in form of a postdoc can bring many advantages for future career goals in academia as well as in industry.¹ However, the decision whether to seek a postdoctoral position should be well conceived. A previous study suggests that ten years after accomplishing a PhD the average ex-postdoc salary is lower than for non-postdocs.² Nevertheless, this study was conducted solely for biomedical studies in the United States and might be different in other countries and for other research fields. Furthermore, a postdoc experience is not only useful to learn new skill sets in a foreign research environment but can also help to acquire a great set of soft skills.

As a current German postdoc in the United States, I would like to outline several factors that can lead to a positive US postdoc experience. First, it is important to start to plan early before the end of the PhD since finding the right group as well as the bureaucratic process can take a lot of time. I recommend planning at least 1 year in advance. The most difficult decision is probably which research institute and group to apply to. In this context, I agree with previous studies that underline the importance of the research environment, collaborations, and quality of supervision for beneficial postdoctoral training.¹ Therefore, the receiving research institute and group needs to be selected with care and it can be helpful to inquire whether the department has a great research network with other research groups or has engaged in various collaborations in the past. Furthermore, it can also be beneficial to talk to other group members before accepting a postdoctoral position. They might give valuable insights not only into the quality of the supervision by the principal investigator but also into how well the knowledge transfer within the group has been established.

One of the most important aspects is financial funding. While several research groups might have fully funded postdoctoral positions available, others might require a fully sponsored fellowship from international organizations such as EMBO, HFSB, or national organizations such as the German research foundation (Deutsche Forschungsgemeinschaft) for Germany-based candidates. The fellowship application process can take between 3 and 9 months and requires a lot of effort, particularly during the end of a PhD.

After the successful application and acceptance of a postdoctoral position, the J1-visa application and interview process can take up to several months depending on the location and workload of the embassy. First, the postdoctor

Analytical sciences are among the most dynamically developing fields and have been inherently integrated into many various scientific disciplines. At the same time, early career researchers (ECRs) are among those whose contribution to this dynamic growth cannot be simply overestimated. Hence, in this special issue “From one ECR to the next”, we are presenting a series of editorials with questions and answers from five emerging scientists of different analytical fields including omics, environmental and data sciences. Importantly, all our guests boast not only scientific excellence and high-quality research but also the substantial international experience gained during their PhD or postdoctoral training. For this editorial, we are presenting Dr Sophie Ayciriex.

Dr Sophie Ayciriex obtained a European PhD degree in Biochemistry in 2010 at the University of Bordeaux where she investigated the characterization of new acyltransferases in yeast by reverse genetics and lipidomics analyses by mass spectrometry (MS). During her two post-doc periods, she strengthened her expertise in lipidomics together with MS techniques. She investigated lipidome variations during neurodegenerative processes; lipid-protein interaction and the impact of diet on Drosophila photoreceptors. She is now an associate professor at Univ. Claude Bernard Lyon 1 since 2015, and joined the Institute of Analytical Sciences to develop analytical methods for multi-omics applied to ecotoxicology and clinical research.

I studied biochemistry and structural biology during my university studies in Toulouse. Then I moved towards the dark force of analytical chemistry, learning targeted and high-resolution MS in Bordeaux and Germany, respectively during my PhD. I am at the interface between these two disciplines which allows me to adapt quickly to different research projects. I strengthened my expertise during my two post-doctoral stints and I am doing still mass spec in my daily life in Lyon.

We are currently working on the analytical development of methods to characterize samples at different biological scales – omics, that is, proteomics, lipidomics and metabolomics with different MS pipelines. We focus on data reprocessing to perform the fusion of the different omics datasets. Indeed, we integrate proteomics, metabolomics and lipidomics data and mine the data to see how we can correlate biomolecules with each other and go deeper into the biological interpretation. We have currently exciting projects with clinicians and researchers in ecotoxicology to apply our methodology. We co-developed with a mass spec company a novel acquisition mode in a targeted MS instrument that enables it to perform multiplex analysis and monitor the signal of thousands of molecules (Scout-multiple reaction monitoring [MRM] also called scout-triggered MRM). Very cool!

It is incredible to see how fast the field (omics) is growing and how the technology is improving so rapidly to answer s

Analytical sciences are among the most dynamically developing fields and have been inherently integrated into many various scientific disciplines. At the same time, early career researchers (ECRs) are among those whose contribution to this dynamic growth cannot be simply overestimated. Hence, in this special issue “From one ECR to the next”, we are presenting a series of editorials with questions and answers from five emerging scientists from different analytical fields including omics, environmental and data sciences. Importantly, all our guests boast not only scientific excellence and high-quality research but also the substantial international experience gained during their PhD or postdoctoral training. For this editorial, we are presenting Dr. Fabio P. Gomes.

Dr. Gomes is a Postdoctoral Researcher at the Scripps Research. He holds a Ph.D. in Analytical Chemistry from the University of Queensland. His research interests include the use of innovative mass spectrometry (MS)-based methods to investigate the structure-function relationship of intact proteoforms and their complexoforms withincells. He is currently developing and applying MS approaches to structurally elucidate intact complexoforms (protein complexes formed by intact monomeric proteoform arrangements) in breast cancer cells, and to interrogate intact proteoforms in single cardiomyocyte cells. Proteins adopt multiple proteoforms as a result of various structural changes (e.g. posttranslational modifications [PTMs] and truncations).

I am an Afro-Brazilian citizen and US permanent resident. I was born and raised in Sao Paulo (Brazil), where I completed both my undergraduate degree and a master's degree with graduate research in Pharmaceutical Sciences. I then moved to the University of Queensland (Australia) to complete my PhD in Analytical Chemistry. After graduation, I moved to the United States where I have held postdoctoral positions in two laboratories led by world leader proteomics: first with Dr. Catherine Fenselau at the University of Maryland (2017–2018) and currently with Dr. John R. Yates III at the Scripps Research (2018–present).

I have 2 overaching research goals. My first goal is to develop and improve technologies for probing intact proteoforms and their complexoforms within the intracellular space. My second goal is to apply these technologies to better understand the molecular mechanisms that govern metastatic tumors, drug resistance, and how lipids bind and modulate the biological activities of important drug targets such as membrane proteins. I am excited about the native top-down proteomics (nTDP) strategy I developed to interrogate complexoforms in breast cancer cells. I plan to extend this approach to investigate the hypothesis that the biological actions of estrogen and antiestrogen drugs in the development of metastatic breast tumors and drug resistance are regulated by estrogen receptor alpha (ER-alpha) proteoforms and complexoforms. I am

As a rather recent PhD graduate and still an “early career researcher”, the author wondered what to write about that would be interesting for a young scientist. The answer came while overhearing students in the break room stating, “I wish I had known all that before starting my PhD that would have made everything easier!” – An experience many researchers are very familiar with. From simple tricks for laboratory work to choosing the right software or planning the next career steps, this was a reoccurring theme during the career of the author, who will try to give a short personal overview for young researchers, especially in the analytics and/or natural products field. These topics and lists represent a personal opinion and are neither meant to be all-encompassing nor of course might differ from the experiences of other researchers.

In the treatment of organophosphate poisoning atropine sulphate monohydrate (AT) and obidoxime dichloride (OB) play a vital role. Currently, the Austrian Armed Forces use the DOUBLEPEN OA two-chamber autoinjector (ChemProtect) to administer these two drugs. The autoinjector is a part of military standard equipment as a “Basic CBRN-First Aid Kit” and contains OB and AT with a declared concentration of 220 mg/2 ml and 2 mg/2 ml, respectively. Especially in the two-chamber autoinjectors, it is highly possible that not all the content of the antidote solution is administered when the autoinjector is triggered. The purpose of the study was to analyze one hundred DOUBLEPEN OA autoinjectors from two different production batches (1707068 and 1707067) for volume loss, drug content and uniformity of dosage unit. Uniformity of dosage units, assessed by the content uniformity method (Chapter 2.9.40 of the European Pharmacopeia), requires the calculation of an acceptable value to quantify the uniformity of the drug product. An acceptance value for the first 10 dosage units of 15.0% or below is considered acceptable. The loss of volume was calculated by determining the density and mass of the solution after triggering the autoinjector. A quantitative high-performance liquid chromatography method has been developed and in-house validated for the determination of the content of two drugs. According to International Council for Harmonisation guidelines, the analytical method was proven to be accurate and repeatable. The obtained results show that the average loss of volume after injection was 5%, and the average content of OB and AT for batch 1707068, was 216.5 and 1.9 mg, while for batch 1707067 it was 224.2 and 2.0 mg, respectively. Although the loss of volume and content were observed, the calculated acceptance value for both production batches met the requirements of uniformity of dosage unit by the European Pharmacopeia.

Carla Kirschbaum is a fourth-year PhD student in the group of Prof. Kevin Pagel at the Freie Universität Berlin and the Fritz Haber Institute of the Max Planck Society. She studied chemistry in Berlin and first joined the group in 2017 for her bachelor's thesis. After a study- and research stay in Paris, she returned to Berlin to complete her master's degree and then seamlessly continue with her doctorate. Since her bachelor's thesis, Carla has been exploring mass spectrometry-based techniques for the structural analysis of lipids. She has received numerous grants and awards for her work and is actively involved in the Young Scientists interest group of the German Society for Mass Spectrometry (DGMS) to foster exchange among young researchers in the field of mass spectrometry.

How did you get involved in the field of analytical sciences?

In fact, my university does not have an analytical chemistry division, and therefore it was not until my bachelor's thesis that I got involved in the field of analytical sciences. During my undergraduate studies, we learned the basics of several analytical techniques in order to analyse substances that we synthesized in the organic chemistry lab courses; however, analytical chemistry was mainly regarded as an auxiliary technique for the synthetic chemist. In my second year, I attended the lecture on bioorganic chemistry by Prof. Kevin Pagel, which became my favourite course in my entire undergraduate studies. Afterwards, Kevin Pagel offered me to do my bachelor's thesis in his group where I got my first hands-on experience with mass spectrometers. In his lab, which is partly located at the Fritz Haber Institute of the Max Planck Society, I used electrospray-mass spectrometry hyphenated with ion mobility spectrometry to study isomeric phospholipids. Although the project did not yield the desired results, my interest in mass spectrometry and lipid analysis had been sparked. In the following year, when I moved to Paris for my master's studies, I continued to work in the field of mass spectrometry. As part of a research internship, I got to know other types of mass spectrometers and ionization techniques at the mass spectrometry platform of Sorbonne Université. In the lab of Prof. Sandrine Sagan, I studied the interactions between cell-penetrating peptides and membrane lipids by crosslinking mass spectrometry.¹

What is the topic of your PhD studies?

After my return from Paris, I finished my master's studies in Berlin and rejoined the Pagel lab for my master's thesis, which laid the groundwork for my PhD thesis. During my master's thesis, I was trained on an instrument developed in the group of Prof. Gert von Helden at the Fritz Haber Institute which combines mass spectrometry and infrared ion spectroscopy. Gas-phase infrared spectra of mass-to-charge-selected ions are obtained by encapsulating the ions in superfluid helium droplets and monitoring the r

Introduction

Kim Greis is a third-year PhD candidate in the lab of Prof. Kevin Pagel at Freie Universität Berlin and Fritz Haber Institute of the Max Planck Society. He joined Humboldt-Universität zu Berlin in 2014 for his bachelor's studies in chemistry and stayed there for his master's degree. During the latter, he went as an exchange student to the University of Melbourne for a research stay. In 2019, he switched to Freie Universität Berlin to start a PhD project in the group of Prof. Kevin Pagel to study reactive intermediates from bioorganic reactions using mass spectrometry-based methods and density-functional theory calculations. Despite his young career he has already published 21 papers (and counting) and collected numerous prestigious awards, such as a Fulbright Grant, which allowed him to do research at Yale University during his PhD.

How did you get involved in the field of analytical sciences?

I did my bachelor's and master's studies at the Humboldt-Universität zu Berlin. In contrast to other chemistry departments, there is a big analytical division at Humboldt-Universität zu Berlin. Hence, a large selection of mandatory analytical chemistry courses was available. For my bachelor thesis, I joined the lab of Prof. Klaus Rademann and developed a cellulose-based sensor to detect low concentrations of toxic metal ions in aqueous solutions.¹ During my master's studies, I switched fields during an exchange internship at the University of Melbourne, where I joined the lab of Prof. Richard O'Hair. Here, I got hands-on experience with mass spectrometers for the first time. We used a modified ion trap mass spectrometer that allows for ion-molecule reactions to study phenanthroline-ligated transition state metal complexes. With this setup, we got information on the reactivity of these species and in some cases, we were able to reveal catalytic cycles.^{2, 3} Furthermore, I learned in Australia about using computational methods, such as density-functional theory, to support my data from mass spectrometry. Subsequently, I joined the lab of Kevin Pagel at Freie Universität Berlin and the Fritz Haber Institute of the Max Planck Society for my master's thesis and stayed there for my PhD.

What is the topic of your PhD studies?

In my PhD studies, I combine computational methods and cryogenic vibrational spectroscopy in helium nanodroplets to investigate the structure of reactive intermediates. Cryogenic vibrational spectroscopy of ions is a mass spectrometry-based technique that I will introduce in a moment. The method yields highly resolved infrared spectra that, in combination with computed frequencies, are very suitable to determine the structure of ions. We used the technique mainly to study glycosyl cations, the reactive intermediate of glycosynthesis.^4-6 In a second step, we correlate the structure with the stereosele