True single-cell proteomics using advanced ion mobility mass spectrometry

In this thesis, I present the development of a novel mass spectrometry (MS) platform and scan modes in conjunction with a versatile and robust liquid chromatography (LC) platform, which addresses current sensitivity and robustness limitations in MS-based proteomics. I demonstrate how this technology benefits the high-speed and ultra-high sensitivity proteomics studies on a large scale. This culminated in the first of its kind label-free MS-based single-cell proteomics platform and its application to spatial tissue proteomics. I also investigate the vastly underexplored ‘dark matter’ of the proteome, validating novel microproteins that contribute to human cellular function. First, we developed a novel trapped ion mobility spectrometry (TIMS) platform for proteomics applications, which multiplies sequencing speed and sensitivity by ‘parallel accumulation – serial fragmentation’ (PASEF) and applied it to first high-sensitivity and large-scale projects in the biomedical arena. Next, to explore the collisional cross section (CCS) dimension in TIMS, we measured over 1 million peptide CCS values, which enabled us to train a deep learning model for CCS prediction solely based on the linear amino acid sequence. We also translated the principles of TIMS and PASEF to the field of lipidomics, highlighting parallel benefits in terms of throughput and sensitivity. The core of my PhD is the development of a robust ultra-high sensitivity LC-MS platform for the high-throughput analysis of single-cell proteomes. Improvements in ion transfer efficiency, robust, very low flow LC and a PASEF data independent acquisition scan mode together increased measurement sensitivity by up to 100-fold. We quantified single-cell proteomes to a depth of up to 1,400 proteins per cell. A fundamental result from the comparisons to single-cell RNA sequencing data revealed that single cells have a stable core proteome, whereas the transcriptome is dominated by Poisson noise, emphasizing the need for both complementary technologies. Building on our achievements with the single-cell proteomics technology, we elucidated the image-guided spatial and cell-type resolved proteome in whole organs and tissues from minute sample amounts. We combined clearing of rodent and human organs, unbiased 3D-imaging, target tissue identification, isolation and MS-based unbiased proteomics to describe early-stage β-amyloid plaque proteome profiles in a disease model of familial Alzheimer’s. Automated artificial intelligence driven isolation and pooling of single cells of the same phenotype allowed us to analyze the cell-type resolved proteome of cancer tissues, revealing a remarkable spatial difference in the proteome. Last, we systematically elucidated pervasive translation of noncanonical human open reading frames combining state-of-the art ribosome profiling, CRISPR screens, imaging and MS-based proteomics. We performed unbiased analysis of small novel proteins and prove their physical existence by LC-MS as HLA peptides, essential interaction partners of protein complexes and cellular function

An author keyword analysis for mapping Sport Sciences

[EN] Scientific production has increased exponentially in recent years. It is necessary to find methodological strategies for understanding holistic or macro views of the major research trends developed in specific fields. Data mining is a useful technique to address this task. In particular, our study presents a global analysis of the information generated during last decades in the Sport Sciences Category (SSC) included in the Web of Science database. An analysis of the frequency of appearance and the dynamics of the Author Keywords (AKs) has been made for the last thirty years. Likewise, the network of co-occurrences established between words and the survival time of new words that have appeared since 2001 has also been analysed. One of the main findings of our research is the identification of six large thematic clusters in the SSC. There are also two major terms that coexist ('REHABILITATION' and 'EXERCISE') and show a high frequency of appearance, as well as a key behaviour in the calculated co-occurrence networks. Another significant finding is that AKs are mostly accepted in the SSC since there has been high percentage of new terms during 2001-2006, although they have a low survival period. These results support a multidisciplinary perspective within the Sport Sciences field of study and a colonization of the field by rehabilitation according to our AK analysis.González-Moreno, L.; García-Massó, X.; Pardo-Ibáñez, A.; Peset Mancebo, MF.; Devis Devis, J. (2018). An author keyword analysis for mapping Sport Sciences. PLoS ONE. 13(8). https://doi.org/10.1371/journal.pone.0201435S13

CIFRA: Challenging the ICT Patent Framework for Responsible Innovation. D4.3: Paper to well-recognized journals

The European Commission. CIFRA: Challenging the ICT Patent Framework for Responsible Innovation. Grant Agreement No.731940. Research and Innovation Action. Call: H2020-ICT-35-201

Human papillomavirus detection by whole-genome next-generation sequencing : importance of validation and quality assurance procedures

Funding: This work was funded by the Center for Innovative Medicine (CIMED grant number 613/06, to KS), the Swedish Medical Society (SLS, grant number 885941, to KS),and the Swedish Foundation for Strategic Research (grant number RB13-0011, supporting KS and SAM). The SHPVRL is supported by National Services Division of the National Health Service in Scotland.Next-generation sequencing (NGS) yields powerful opportunities for studying human papillomavirus (HPV) genomics for applications in epidemiology, public health, and clinical diagnostics. HPV genotypes, variants, and point mutations can be investigated in clinical materials and described in previously unprecedented detail. However, both the NGS laboratory analysis and bioinformatical approach require numerous steps and checks to ensure robust interpretation of results. Here, we provide a step-by-step review of recommendations for validation and quality assurance procedures of each step in the typical NGS workflow, with a focus on whole-genome sequencing approaches. The use of directed pilots and protocols to ensure optimization of sequencing data yield, followed by curated bioinformatical procedures, is particularly emphasized. Finally, the storage and sharing of data sets are discussed. The development of international standards for quality assurance should be a goal for the HPV NGS community, similar to what has been developed for other areas of sequencing efforts including microbiology and molecular pathology. We thus propose that it is time for NGS to be included in the global efforts on quality assurance and improvement of HPV-based testing and diagnostics.Publisher PDFPeer reviewe

On the role of secondary pions in spallation targets

We use particle-transport simulations to show that secondary pions play a crucial role for the development of the hadronic cascade and therefore for the production of neutrons and photons from thick spallation targets. In particular, for the n_TOF lead spallation target, irradiated with 20 GeV/c protons, neutral pions are involved in the production of ~90% of the high-energy photons; charged pions participate in ~40% of the integral neutron yield. Nevertheless, photon and neutron yields are shown to be relatively insensitive to large changes of the average pion multiplicity in the individual spallation reactions. We characterize this robustness as a peculiar property of hadronic cascades in thick targets.Comment: 17 pages, 14 figures. Submitted to Eur. Phys. J.

Big Data and Artificial Intelligence in Digital Finance

This open access book presents how cutting-edge digital technologies like Big Data, Machine Learning, Artificial Intelligence (AI), and Blockchain are set to disrupt the financial sector. The book illustrates how recent advances in these technologies facilitate banks, FinTech, and financial institutions to collect, process, analyze, and fully leverage the very large amounts of data that are nowadays produced and exchanged in the sector. To this end, the book also describes some more the most popular Big Data, AI and Blockchain applications in the sector, including novel applications in the areas of Know Your Customer (KYC), Personalized Wealth Management and Asset Management, Portfolio Risk Assessment, as well as variety of novel Usage-based Insurance applications based on Internet-of-Things data. Most of the presented applications have been developed, deployed and validated in real-life digital finance settings in the context of the European Commission funded INFINITECH project, which is a flagship innovation initiative for Big Data and AI in digital finance. This book is ideal for researchers and practitioners in Big Data, AI, banking and digital finance

Prijedlog ontološki utemeljenog metodološkog okvira za razvoj više-platformskih mobilnih aplikacija

Software development teams are faced with the lack of interoperability during the development of mobile applications for two or more target platforms. The development for second and every other platform means a new project with a need to repeat almost all the phases defined by the chosen methodology but with a narrow possibility of reuse of the already defined artifacts. The existing efforts of professional and scientific community to solve this problem have a similar approach (code once, run everywhere) with similar advantages and drawbacks. Thus, this dissertation aims to propose a different solution and is concerned with: (1) analyzing the methodologies suitable for mobile applications development, (2) observing the implementation of prototype application in order to define artifacts that are created during the development process for two target platforms, (3) semantic description of artifacts and their meaning, and (4) defining unique ontological definition as a base for methodological interoperability. The results of a systematic literature review performed on 6761 primary studies, show that current state-of-the-art literature brings only 22 development methodologies and 7 development approaches which can be identified as eligible for multi-platform mobile applications development. Among these, Mobile-D methodology accompanied with Test Driven Development was chosen and used in the observed development processes for Android and Windows Phone platforms. Total of 71 artifacts were identified and the artifacts reusability level when developing for second target platform was 66.00%. In the last research phase, the artifacts for both platforms were semantically described into a single ontological description comprising 213 classes, 14 object properties and 2213 axioms defined in ALCRIF DL expression sub-language. Having this ontology proved as correct and valid, flexible, reusable and extensible we created the basis for development of an information system to guide the development teams in a more efficient and interoperable process of multiplatform mobile applications development.Razvojni timovi susreću se s problemom neinteroperabilnosti prilikom razvoja aplikacija za dvije ili više mobilnih platformi. Razvoj aplikacije za drugu i svaku sljedeću platformu znači novi projekt u kojem je potrebno ponovno provesti većinu faza definiranih odabranom metodikom razvoja, pri čemu se kreirani artefakti teško ili uopće ponovno ne koriste. Napori profesionalne i znanstvene zajednice za rješenjem ovog problema imaju sličan pristup (kodiraj jednom, koristi svugdje), slične prednosti, ali i zajedničke nedostatke. Stoga ova disertacija navedenom problemu pristupa na nov način i bavi se: (1) analiziranjem metodika pogodnih za razvoj mobilnih aplikacija, (2) promatranjem razvoja prototipne aplikacije u svrhu definiranja artefakata koji nastaju pri razvoju mobilne aplikacije za dvije ciljane platforme, (3) semantičkim opisivanjem definiranih artefakata i njihovih značenja, te (4) definiranjem jedinstvene ontološke definicije kao osnove za metodološku interoperabilnost. Rezultati sustavnog pregleda literature provedenog nad 6761 radom pokazali su da se trenutno u literaturi spominju 22 metodike i 7 pristupa koji su pogodni za razvoj više-platformskih mobilnih aplikacija. Između identificiranih metodika odabrani su Mobile-D metodika i pristup razvoju vođen testiranjem, koji su korišteni pri implementaciji prototipnog rješenja za Android i Windows Phone platformu. Ukupno je identificiran 71 artefakt pri čemu je ponovna iskoristivost artefakata pri razvoju za drugu platformu bila 66.00%. U posljednjoj su fazi istraživanja artefakti semantički opisani u zajedničku ontološku definiciju koja u konačnici sadrži 213 klasa, 14 objektnih svojstava i 2213 aksioma definiranih pomodu ALCRIF-DL jezika izraza. U radu je dokazano da je ontologija valjana, fleksibilna, ponovno iskoristiva i nadogradiva, čime je kreirana osnova za razvoj informacijskog sustava koji bi vodio razvojne timove u efikasnijem i bolje interoperabilnom procesu razvoja više-platformskih mobilnih aplikacija

Prijedlog ontološki utemeljenog metodološkog okvira za razvoj više-platformskih mobilnih aplikacija

Software development teams are faced with the lack of interoperability during the development of mobile applications for two or more target platforms. The development for second and every other platform means a new project with a need to repeat almost all the phases defined by the chosen methodology but with a narrow possibility of reuse of the already defined artifacts. The existing efforts of professional and scientific community to solve this problem have a similar approach (code once, run everywhere) with similar advantages and drawbacks. Thus, this dissertation aims to propose a different solution and is concerned with: (1) analyzing the methodologies suitable for mobile applications development, (2) observing the implementation of prototype application in order to define artifacts that are created during the development process for two target platforms, (3) semantic description of artifacts and their meaning, and (4) defining unique ontological definition as a base for methodological interoperability. The results of a systematic literature review performed on 6761 primary studies, show that current state-of-the-art literature brings only 22 development methodologies and 7 development approaches which can be identified as eligible for multi-platform mobile applications development. Among these, Mobile-D methodology accompanied with Test Driven Development was chosen and used in the observed development processes for Android and Windows Phone platforms. Total of 71 artifacts were identified and the artifacts reusability level when developing for second target platform was 66.00%. In the last research phase, the artifacts for both platforms were semantically described into a single ontological description comprising 213 classes, 14 object properties and 2213 axioms defined in ALCRIF DL expression sub-language. Having this ontology proved as correct and valid, flexible, reusable and extensible we created the basis for development of an information system to guide the development teams in a more efficient and interoperable process of multiplatform mobile applications development.Razvojni timovi susreću se s problemom neinteroperabilnosti prilikom razvoja aplikacija za dvije ili više mobilnih platformi. Razvoj aplikacije za drugu i svaku sljedeću platformu znači novi projekt u kojem je potrebno ponovno provesti većinu faza definiranih odabranom metodikom razvoja, pri čemu se kreirani artefakti teško ili uopće ponovno ne koriste. Napori profesionalne i znanstvene zajednice za rješenjem ovog problema imaju sličan pristup (kodiraj jednom, koristi svugdje), slične prednosti, ali i zajedničke nedostatke. Stoga ova disertacija navedenom problemu pristupa na nov način i bavi se: (1) analiziranjem metodika pogodnih za razvoj mobilnih aplikacija, (2) promatranjem razvoja prototipne aplikacije u svrhu definiranja artefakata koji nastaju pri razvoju mobilne aplikacije za dvije ciljane platforme, (3) semantičkim opisivanjem definiranih artefakata i njihovih značenja, te (4) definiranjem jedinstvene ontološke definicije kao osnove za metodološku interoperabilnost. Rezultati sustavnog pregleda literature provedenog nad 6761 radom pokazali su da se trenutno u literaturi spominju 22 metodike i 7 pristupa koji su pogodni za razvoj više-platformskih mobilnih aplikacija. Između identificiranih metodika odabrani su Mobile-D metodika i pristup razvoju vođen testiranjem, koji su korišteni pri implementaciji prototipnog rješenja za Android i Windows Phone platformu. Ukupno je identificiran 71 artefakt pri čemu je ponovna iskoristivost artefakata pri razvoju za drugu platformu bila 66.00%. U posljednjoj su fazi istraživanja artefakti semantički opisani u zajedničku ontološku definiciju koja u konačnici sadrži 213 klasa, 14 objektnih svojstava i 2213 aksioma definiranih pomodu ALCRIF-DL jezika izraza. U radu je dokazano da je ontologija valjana, fleksibilna, ponovno iskoristiva i nadogradiva, čime je kreirana osnova za razvoj informacijskog sustava koji bi vodio razvojne timove u efikasnijem i bolje interoperabilnom procesu razvoja više-platformskih mobilnih aplikacija