News and Views from a Mass Spectrometry Lab in Irapuato, Mexico

My Sabbath Year (2018-2019)

"25 The Lord said to Moses at Mount Sinai, 2 “Speak to the Israelites and say to them: ‘When you enter the land I am going to give you, the land itself must observe a sabbath to the Lord. 3 For six years sow your fields, and for six years prune your vineyards and gather their crops. 4 But in the seventh year the land is to have a year of sabbath rest, a sabbath to the Lord. Do not sow your fields or prune your vineyards. 5 Do not reap what grows of itself or harvest the grapes of your untended vines. The land is to have a year of rest. 6 Whatever the land yields during the sabbath year will be food for you—for yourself, your male and female servants, and the hired worker and temporary resident who live among you, 7 as well as for your livestock and the wild animals in your land. Whatever the land produces may be eaten." (Leviticus 25:1-7, New International Version)

Half a year after returning from my sabbatical year, I believe having enough distance to write about my experiences.

What is the idea of a sabbatical?

Time is our most precious good, and as successful scientists, we tend to optimize our efficiency and output. Since we finish more and more work in less time, we are famous victims for accepting even more responsibilities (e.g., in editorial boards, teaching, funding review activities). We continue this vicious cycle until any little disturbance (unexpected visitors, traffic jams, internet problems, canceled school classes) causes us a high level of stress. The increasing pressure to publish ("a lot and high impact," of course) and to find funding keeps us busy. We can hold this rhythm for several years without slowing down. However, our family, social, and cultural life suffer if we answer 'important' Emails at night. And since we never learned how to shift down and reduce our speed, we are in danger of overheating and burn-out.

A sabbatical break gives us the chance to leave the hamster's wheel temporarily and to recharge batteries. And in the best case, we learn strategies for a more sustainable life.

The offer by our institution

Our research institution, The Center for Research and Advanced Studies of the National Polytechnic Institute (CINVESTAV) allows us to work every seventh year in another institution. The procedure is pretty simple, and during our sabbatical, our salary is fully paid. Our institutional duties, such as participation in committees, are paused or reduced to a minimum. We have complete freedom to choose a country and institution for a stay of one year.

Our host 'Max Planck', teaching and research

My wife Laila Pamela Partida Martínez and I were accepted as visiting scientists by the research groups of Ian Baldwin and Ales Svatos, respectively, at the Max Planck Institute for Chemical Ecology (Jena, Germany). Many thanks to them for their hospitality!

The MPI has all the infrastructure you can dream of. Thus, I did some experiments, e.g., mounting our 3D-printed low-temperature plasma (3D-LTP) probe on a Prosolia DESI platform (the MPI workshop built a little adaptor for me). Since I connected our 3D-LTP probe for the first time to an Orbitrap mass analyzer, I was quite happy with the analytical resolution. At least one paper should be coming out from that. As well, I had the opportunity to visit my collaborator of the BAM Berlin in our joint Conacyt-DFG project, Jens Riedel. It was awesome to see his laser toys and gadgets. However, my main research activity was related to mass spectrometry data processing and data mining. For example, I learned how to employ Docker for mass spectrometry workflows and how to post-process prot.xml files with Python.

Further, I participated in giving a course in "Computational Mass Spectrometry" for the "International Max Planck Research School (IMPRS)" students. The interaction with the group also allowed me to test an R script for XCMS and a chapter for the RSC book mentioned below.

I enjoyed the international atmosphere (especially in the coffee room), and I made new contacts. The collaboration with the ICE mass spectrometry group is ongoing, especially with Natalie Wielsch (thanks for all the chocolate!), an expert in plant proteomics.

Family and daily life

Our boys were 8 and 11 years old when we moved to Jena. Both grew up in Mexico; thus, their German language level was modest. Fortunately, they were accepted by the Montessori School Jena. We appreciate all the support from their teachers because the children were quickly integrated and made great progress. Both countries accepted the completed school years of the other country. Of course, some classes were different. E.g., the Thuringian kids have to know the alibi name of Martin Luther while he was hidden in the Wartburg - 'Junker Jörg.' In contrast, Mexican kids learn about the battle of Puebla, which is celebrated on the 5th of May. But since the Montessori philosophy is based on the inherent curiosity of children and guided activities, the kids were optimally promoted.

Before the sabbatical year, we sold our car, and in Jena, we bought used bicycles. The weekend shopping was limited to the capacity of my bike trailer, which helped to prevent the buying of unnecessary stuff and junk food. During the wintertime, biking was not always pleasant. Especially for going to school (~6 km). Nevertheless, the boys were pretty tough, and only on some icy days with snow on the road, they used the bus. In the beginning, we accompanied the children when biking to school. But later, they moved independently in the city.

It was a change for us, to live as a family of only four, without close-by grandparents or 'helping hands.' Therefore, we had to organize cooking, household, and laundry. However, it can be quite productive to stay at home for soldering a prototype, writing or programming, waiting until the washing machine is ready, and the cloths can be hanged for drying (either in the drying room or outside in the garden!).

Since we had a park and playground (Friedensberg, Jena) just in front of our house, we frequently played soccer and frisbee. Unfortunately, just going out to play is not so easy in Irapuato because we need to go by car to fields for outdoor sports. As well, we had more family time during our sabbatical year, which we enjoyed a lot.

As well, I learned shaving with a straight razor, and some days I left the bathroom with a cut. However, now I am free of expensive and waste-creating system razors!

Traveling between continents and maintaining two houses is, of course, somehow costly. Nevertheless, this was not too critical, because several services we pay in Mexico, e.g., the school, were for free in Germany. The health insurance was kind of challenging. Finally, we contracted private health insurance with coverage abroad in Mexico. Importantly, many countries got tax laws for temporal academic stays. The Jena Finanzamt (taxation office) was very helpful in resolving our questions for avoiding double taxation. In general, the authorities in Jena were very helpful for all our administrative tasks (registration/ migration/ taxation/ school, etc.). Anyway, before moving with a family, one should consider several months of planning.

Friends, culture and social life

I studied my first degree in Jena, and my wife and I came back for Ph.D. and PostDoc. Thus, we already knew many people, which facilitated our re-integration. For example, our friend Agnes borrowed us an electronic piano for the year and we made several weekend trips with her family. Thanks a lot, Agnes!

Arriving at Jena, I started again playing the trumpet. When I was a student, I was a member of the Dixielanders. 'Duddle,' their former tuba player (and now a member of BlechARTig quickly 'contracted' me for some Christmas combos. The same Duddle now will visit us in Irapuato; during his sabbatical world travel.

As well, I participated in the Max Planck orchestra and the Bavarian Musikkapelle Emmerting, where I was a co-founder more than 30 years ago, and practiced improvisation.

From time to time, I met old friends to discuss life with a beer (or two), or to watch a horror movie.

Since everything is close and well-connected in Europe, we organized a reunion with our friends from the time we studied our Master's in Birmingham, UK. We met in the house of an Italian friend that is now married to a Belgian. Our other friends came from France, England (married with a Mexican), and Indonesia. We enjoyed Belgian beer and chocolate, and we had a great time. Thanks, Susi & the Brummy family!

During the sabbatical, I also found out that Yoga is not for me ;-).

Book writing

For several years I wanted to start a Wiki about mass spectrometry (MS) data processing. I published an open-access article on biological MS workflows and advanced statistics (PeerJ, 2015), but never managed to compile a comprehensive work.

Thus, as Marek Domin (Boston College, US) asked me if I wanted to edit a book on Metabolomics for the Royal Society of Chemistry, I immediately accepted. The first draft of the book proposal I wrote on my cell phone, waiting for the kids, on a bench close to the Montessori school. Fortunately, it was summer (2018). Finally, we expanded the scope and also included Proteomics and MS data processing toolkits.

I warmly thank all the authors that contributed to the book (in the order of appereance): Magnus Palmblad, David S. Wishart, Joanna Godzien, Alberto Gil de la Fuente, Rupasri Mandal, Rahmatollah Rajabzadeh, Hamed Pirimoghadam, Carol Ladner-­Keay, Abraham Otero, Coral Barbas, Marc Vaudel, Miguel Reboiro-­Jato, Daniel Glez-­Peña, Hugo López-­Fernández, Oliver Alka, Timo Sachsenberg, Leon Bichmann, Julianus Pfeuffer, Hendrik Weisser, Samuel Wein, Eugen Netz, Marc Rurik, Oliver Kohlbacher, Hannes Röst, Tomáŝ Pluskal, Ansgar Korf, Aleksandr Smirnov, Robin Schmid, Timothy R. Fallon, Xiuxia Du, Jing-­Ke Weng, Laila Pamela Partida-Martí­nez, Bo Wen, Eric W. Deutsch, Luis Mendoza, David D. Shteynberg, Zhi Sun, Michael H. Hoopmann, Robert L. Moritz, Kaikun Xu, Cheng Chang, Cesaré Ovando-­Vázquez, Nils Hoffmann, Yasset Perez-­Riverol, Olivier Sallou and Björn A. Grüning.

Now, in March 2020, finally, the book is available from the Royal Society of Chemistry with the title "Processing Metabolomics and Proteomics Data with Open Software: A Practical Guide."

I am very proud and satisfied with the book, and much appreciate the support of all authors, Marek and the RSC (Janet Freshwater and Katie Morrey). Writing my first textbook was a fantastic experience!

Technology transfer and product development

In 2018, my wife and I created a spin-off company (Kuturabi SA de CV) for facilitating the technology transfer of our labs, such as the Open LabBot, the 3D-LTP, and our ambient ionization mass spectrometry imaging system. During the sabbatical year, I met future collaboration partners and experts for the technical requirements of electronic devices in the European Union.

Further, I started playing with Arduino and Wemos microcomputers and developed little devices for environmental monitoring (climate and volatile organic compounds, VOCs). During this year, I advanced quickly, from first (very ugly) experimental circuits to professional PCBs with Internet-of-Things capability. This project is now running on its own, and we will continue to develop the MeteoMex platform as a community kit.

Although our primary interest is academic and not a business, I can see significant progress in the consolidation of our company.

What happened to my laboratory in Mexico?

I have to admit that I felt somehow guilty to leave my research group labABI on its own for one year. Of course, we kept in contact by email and weekly reports (;-)), but the daily communication and coffee were missing. My colleague Alejandro Blanco (Many thanks!!) supervised the group during this time and supported us in case of administrative tasks and problems. During my absence, one last-year Ph.D. student left the lab to become a solopreneur in organic foods. Although this is a pity for the postgraduate program, he looks happy when I meet him at the institute or in the city. Two PhDs and one M.Sc. student of the labABI graduated shortly after my return and found jobs. In all aspects, the productivity of the laboratory was higher than in years with my physical presence.

Impact on physical and mental health

Despite a typical Bavarian/ German "diet" during the sabbatical, my metabolic status (cholesterol, triglycerides, etc.) improved significantly, which indicates that stress indeed affects your (objectively measurable) health. I recognized that nothing critical happens if I am not always available. Now, I just hope to keep that in mind for avoiding future self-exploitation.

Coming home and being 'guest.'

If you return after more than ten years living abroad to your homeland, this situation is kind of weird. Maybe comparable to returning to your parents' house after a long absence. You know all the furniture and the taste of the food, but anyhow you feel more like a guest than really belonging there.

It is never valid to compare two countries, but I could compare Germany when we left it in 2008 and today. To my impression, the social system and public services, such as the train system, notably reduced their quality. The country, which is based on technology and knowledge, lost leadership in comparison to other countries such as China. In science, we can see the rise of China very clearly and taking away an editorial bias; the picture would be even more drastic. Europe and the US are becoming less important in the future world, and maybe it's time to recognize that fact.

This is not a political blog, but I hope that global development will go towards collaboration and social and economic fairness. Anyhow, I think it would be a pleasant experience for political leaders to live other realities, such as other countries or social environments—for example, a sabbatical as an unemployed or migrant. Only changing the perspective can reveal new insights.


The sabbatical year was rich in experiences and more fertile than just another 'routine' year.

Even if you consider yourself indispensable at work, you should do it!

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