Quality Metrics and Reordering Strategies for Revealing Patterns in BioFabric Visualizations

Visualizing relational data is crucial for understanding complex connections between entities in social networks, political affiliations, or biological interactions. Well-known representations like node-link diagrams and adjacency matrices offer valuable insights, but their effectiveness relies on the ability to identify patterns in the underlying topological structure. Reordering strategies and layout algorithms play a vital role in the visualization process since the arrangement of nodes, edges, or cells influences the visibility of these patterns. The BioFabric visualization combines elements of node-link diagrams and adjacency matrices, leveraging the strengths of both, the visual clarity of node-link diagrams and the tabular organization of adjacency matrices. A unique characteristic of BioFabric is the possibility to reorder nodes and edges separately. This raises the question of which combination of layout algorithms best reveals certain patterns. In this paper, we discuss patterns and anti-patterns in BioFabric, such as staircases or escalators, relate them to already established patterns, and propose metrics to evaluate their quality. Based on these quality metrics, we compared combinations of well-established reordering techniques applied to BioFabric with a well-known benchmark data set. Our experiments indicate that the edge order has a stronger influence on revealing patterns than the node layout. The results show that the best combination for revealing staircases is a barycentric node layout, together with an edge order based on node indices and length. Our research contributes a first building block for many promising future research directions, which we also share and discuss. A free copy of this paper and all supplemental materials are available at https://osf.io/9mt8r/?view_only = b70dfbe550e3404f83059afdc60184c6.

Hybridization and reticulate evolution in Diphasiastrum (flat-branched clubmosses, Lycopodiaceae) - New data from the island of Taiwan and Vietnam

In the species groups related to Diphasiastrum multispicatum and D. veitchii, hybridization was investigated in samples from northern and southern Vietnam and the island of Taiwan, including available herbarium specimens from southeast Asia. The accessions were analyzed using flow cytometry (living material only), Sanger sequencing and multiplexed inter-simple sequence repeat genotyping by sequencing. We detected two cases of ancient hybridization involving different combinations of parental species; both led via subsequent duplication to tetraploid taxa. A cross D. multispicatum × D. veitchii from Malaysia represents D. wightianum, a tetraploid taxon according to reported DNA content measurements of dried material (genome formulas MM, VV and MMVV, respectively). The second case involves D. veitchii and an unknown diploid parent (genome formula XX). Three hybridogenous taxa (genome formulas VVX, VVXX, VVVX) were discernable by a combination of flow cytometry and molecular data. Taxon I (VVX, three clones found on Taiwan island) is apparently triploid. Taxon II represents another genetically diverse and sexual tetraploid species (VVXX) and can be assigned to D. yueshanense, described from Taiwan island but occurring as well in mainland China and Vietnam. Taxon III is as well most likely tetraploid (VVVX) and represented by at least one, more likely two, clones from Taiwan island. Taxa I and III are presumably asexual and new to science. Two independently inherited nuclear markers recombine only within, not between these hybrids, pointing towards reproductive isolation. We present an evolutionary scheme which explains the origin of the hybrids and the evolution of new and fully sexual species by hybridization and subsequent allopolyploidization in flat-branched clubmosses.

Handheld methanol detector for beverage analysis: interlaboratory validation

Methanol is a toxic alcohol contained in alcoholic beverages as a natural byproduct of fermentation or added intentionally to counterfeits to increase profit. To ensure consumer safety, many countries and the EU have established strict legislation limits for methanol content. Methanol concentration is mostly detected by laboratory instrumentation since mobile devices for routine on-site testing of beverages in distilleries, at border stations or even at home are not available. Here, we validated a handheld methanol detector for beverage analysis in an ISO 5725 interlaboratory trial: a total of 119 measurements were performed by 17 independent participants (distilleries, universities, authorities, and competence centers) from six countries on samples with relevant methanol concentrations (0.1, 1.5 vol%). The detector was based on a microporous separation filter and a nanostructured gas sensor allowing on-site measurement of methanol down to 0.01 vol% (in the liquid) within only 2 min by laymen. The detector showed excellent repeatability (<5.4%), reproducibility (<9.5%) and small bias (<0.012 vol%). Additional measurements on various methanol-spiked alcoholic beverages (whisky, rum, gin, vodka, tequila, port, sherry, liqueur) indicated that the detector is not interfered by environmental temperature and spirit composition, featuring excellent linearity (R2 > 0.99) down to methanol concentrations of 0.01 vol%. This device has been recently commercialized (Alivion Spark M-20) with comparable accuracy to the gold-standard gas chromatography and can be readily applied for final product inspection, intake control of raw materials or to identify toxic counterfeit products.

TreEducation: A Visual Education Platform for Teaching Treemap Layout Algorithms

Treemaps are a powerful tool for representing hierarchical data in a space-efficient manner and are used in various domains, including network security or software development. However, interpreting the topology encoded by nested rectangles can be challenging, particularly compared to tree-structured representations like node-link diagrams or icicle plots. To address this challenge, we introduce TreEducation, a visual education platform designed to improve the visualization literacy skills required for reading treemaps among non-expert users. TreEducation is an online application that combines visualizations, interactions, and gamification elements to facilitate understanding of eight different treemap layout algorithms and enhance students' learning process. We evaluated TreEducation in a classroom setting and a controlled environment. Our results indicate a significant knowledge gain of students training exclusively with TreEducation and the usefulness of competition as a social gamification element included in our competitive quiz.

Corrective osteotomy of the distal radius with palmar locking plate osteosynthesis without bone grafting and without cortical contact

The aim of this study was to assess bone healing and secondary fracture displacement after corrective osteotomy of the distal radius without any cortical contact using palmar locking plates without bone grafting. Between 2009 and 2021, 11 palmar corrective osteotomies of extra-articular malunited distal radius fractures and palmar plate fixations without the use of bone grafts and without cortical contact, were assessed. All patients showed complete osseous restoration and significant improvement in all radiographic parameters. Except for one patient, there were no secondary dislocations or loss of reduction in the postoperative follow-up. Bone grafts may not be mandatory for bone healing and prevention of secondary fracture displacement after palmar corrective osteotomy without cortical contact and fixation with palmar locking plate.Level of evidence: IV.

A closer look to the timing of orchidopexy in undescended testes and adherence to the AWMF-guideline

BACKGROUND

To lower the risk of testicular malignancies and subfertility, international guidelines recommend orchidopexy for undescended testis (UDT) before the age of 12-18 months. Previous studies reported low rates of 5-15% of timely surgery. Most of these studies are based on DRG and OPS code-based data from healthcare system institutions that do not distinguish between congenital and acquired UDT.

METHODS

In a retrospective study data of all boys who underwent orchidopexy in a university hospital and two outpatient surgical departments from 2009 to 2022 were analyzed. The data differentiates congenital from acquired UDT.

RESULTS

Out of 2694 patients, 1843 (68.4%) had congenital and 851 (31.6%) had acquired UDT. In 24.9% of congenital cases surgery was performed before the age of 12 months. The median age at surgery for congenital UDT was 16 months (range 7-202). Over the years there was an increased rate of boys operated on before the age of 2 (40% in 2009, 60% in 2022). The median age fluctuated over the years between 21 and 11 months without a trend to younger ages.. The covid pandemic did not lead to an increase of the median age at surgery. The median time between referral and surgery was 46 days (range 1-1836). Reasons for surgery after 12 months of age were a delayed referral to pediatric surgeries (51.2%), followed by relevant comorbidities (28.2%).

CONCLUSION

Compared to recent literature, out data show that a closer look at details enables a more realistic approach. Still, there is no trend towards the recommended age for surgical treatment observable, but the rate of timely operated boys with congenital UDT is significantly higher than stated in literature.

Mucor osteomyelitis after traumatic forearm amputation in a 38-year-old patient

We report the case of a forest ranger who developed a polymicrobial infection with Mucor circinelloides after traumatic forearm amputation. Based on our case report we discuss epidemiology and management of this rare and potentially fatal infection.

[Blunt abdominal trauma in children and adolescents: treatment concepts in the acute phase]

Fatal accidents due to blunt force trauma are the leading cause of death in children and adolescents [1]. Abdominal trauma is the third most common cause of death after traumatic brain injury and thoracic injuries [2]. Abdominal injury is seen in approximately 2-5% of children involved in accidents [3]. Blunt abdominal injuries are common sequelae of traffic accidents (for example as seat belt injury), falls, and sports accidents. Penetrating abdominal injuries are rare in central Europe. Spleen, liver, and kidney lacerations are the most common injuries after blunt abdominal trauma [4]. In most situations, nonoperative management (NOM) has become the gold standard with the surgeon leading the multidisciplinary treatment [5].

Dynamics of Nanosecond Laser Pulse Propagation and of Associated Instabilities in a Magnetized Underdense Plasma

The propagation and energy coupling of intense laser beams in plasmas are critical issues in inertial confinement fusion. Applying magnetic fields to such a setup has been shown to enhance fuel confinement and heating. Here we report on experimental measurements demonstrating improved transmission and increased smoothing of a high-power laser beam propagating in a magnetized underdense plasma. We also measure enhanced backscattering, which our kinetic simulations show is due to magnetic confinement of hot electrons, thus leading to reduced target preheating.

Beyond image defined risk factors (IDRFs): a delphi survey highlighting definition of the surgical complexity index (SCI) in neuroblastoma

PURPOSE

Preoperative evaluation of Image Defined Risk Factors (IDRFs) in neuroblastoma (NB) is crucial for determining suitability for upfront resection or tumor biopsy. IDRFs do not all carry the same weighting in predicting tumor complexity and surgical risk. In this study we aimed to assess and categorize a surgical complexity (Surgical Complexity Index, SCI) in NB resection.

METHODS

A panel of 15 surgeons was involved in an electronic Delphi consensus survey to identify and score a set of shared items predictive and/or indicative of surgical complexity, including the number of preoperative IDRFs. A shared agreement included the achievement of at least 75% consensus focused on a single or two close risk categories.

RESULTS

After 3 Delphi rounds, agreement was established on 25/27 items (92.6%). A severity score was established for each item ranging from 0 to 3 with an overall SCI range varying from a minimum score of zero to a maximum score of 29 points for any given patient.

CONCLUSIONS

A consensus on a SCI to stratify the risks related to neuroblastoma tumor resection was established by the panel experts. This index will now be deployed to critically assign a better severity score to IDRFs involved in NB surgery.

Lung macrophages utilize unique cathepsin K-dependent phagosomal machinery to degrade intracellular collagen

Resident tissue macrophages are organ-specialized phagocytes responsible for the maintenance and protection of tissue homeostasis. It is well established that tissue diversity is reflected by the heterogeneity of resident tissue macrophage origin and phenotype. However, much less is known about tissue-specific phagocytic and proteolytic macrophage functions. Here, using a quantitative proteomics approach, we identify cathepsins as key determinants of phagosome maturation in primary peritoneum-, lung-, and brain-resident macrophages. The data further uncover cathepsin K (CtsK) as a molecular marker for lung phagosomes required for intracellular protein and collagen degradation. Pharmacological blockade of CtsK activity diminished phagosomal proteolysis and collagenolysis in lung-resident macrophages. Furthermore, profibrotic TGF-β negatively regulated CtsK-mediated phagosomal collagen degradation independently from classical endocytic-proteolytic pathways. In humans, phagosomal CtsK activity was reduced in COPD lung macrophages and non-COPD lung macrophages exposed to cigarette smoke extract. Taken together, this study provides a comprehensive map of how peritoneal, lung, and brain tissue environment shapes phagosomal composition, revealing CtsK as a key molecular determinant of lung phagosomes contributing to phagocytic collagen clearance in lungs.

Multiscale Visualization: A Structured Literature Analysis

Multiscale visualizations are typically used to analyze multiscale processes and data in various application domains, such as the visual exploration of hierarchical genome structures in molecular biology. However, creating such multiscale visualizations remains challenging due to the plethora of existing work and the expression ambiguity in visualization research. Up to today, there has been little work to compare and categorize multiscale visualizations to understand their design practices. In this article, we present a structured literature analysis to provide an overview of common design practices in multiscale visualization research. We systematically reviewed and categorized 122 published journal or conference articles between 1995 and 2020. We organized the reviewed articles in a taxonomy that reveals common design factors. Researchers and practitioners can use our taxonomy to explore existing work to create new multiscale navigation and visualization techniques. Based on the reviewed articles, we examine research trends and highlight open research challenges.

The study on health of older people in Germany (Health 65+): Design and first results

Background

Integrating older persons into continuous national public health monitoring is crucial but challenging. Health 65+ is the first national health interview and examination survey in Germany specifically tailored to the needs of the population 65+ years.

Methods

Health 65+ is based on two-stage stratified random sampling from 128 local population registries. It is based on a previously tested three-step procedure to contact the study population (letter, telephone, home visits). 12,448 individuals 65+ years were invited for survey participation between June 2021 and April 2022. Participation comprised answering a baseline-questionnaire/interview covering a consented set of key health indicators including SARS-COV2 infections, and 3 follow-ups. After one year participants are invited to an examination (e.g. blood pressure, grip strength, cognitive function) during a home visit. All-cause mortality, health insurance data and information on social and built environment will be linked to survey data. The preliminary data set comprises 3,107 baseline participants.

Preliminary results

Only few individuals were excluded for survey participation as they had deceased before invitation, moved to an unknown residence or had insufficient German language skills. Of the adjusted gross sample, 32% took part in the survey (47.9% women, mean age 78.8 years). Only 3.3% of the participants did not receive any vaccination against COVID-19, with no differences between gender or age-groups. 3.5% had already experienced a laboratory-confirmed SARS-CoV-2 infection.

Conclusions

Health 65+ collects information that cannot be obtained from any other data sources. In combination with information from routine health data and official health statistics, the results will aid health policy planning and implementation research to improve health and wellbeing of older people in Germany. For example, preliminary results show, that vaccination acceptance was high in persons 65+ years in Germany.

Key messages

• Health 65+ will provide health data of people 65+ years in Germany.

• The results will aid health policy planning.

Stabilized Radiation Pressure Acceleration and Neutron Generation in Ultrathin Deuterated Foils

Premature relativistic transparency of ultrathin, laser-irradiated targets is recognized as an obstacle to achieving a stable radiation pressure acceleration in the "light sail" (LS) mode. Experimental data, corroborated by 2D PIC simulations, show that a few-nm thick overcoat surface layer of high Z material significantly improves ion bunching at high energies during the acceleration. This is diagnosed by simultaneous ion and neutron spectroscopy following irradiation of deuterated plastic targets. In particular, copious and directional neutron production (significantly larger than for other in-target schemes) arises, under optimal parameters, as a signature of plasma layer integrity during the acceleration.

In vivo Characterization of Endogenous Protein Interactomes in Drosophila Larval Brain, Using a CRISPR/Cas9-based Strategy and BioID-based Proximity Labeling

Understanding protein-protein interactions (PPIs) and interactome networks is essential to reveal molecular mechanisms mediating various cellular processes. The most common method to study PPIs in vivo is affinity purification combined with mass spectrometry (AP-MS). Although AP-MS is a powerful method, loss of weak and transient interactions is still a major limitation. Proximity labeling (PL) techniques have been developed as alternatives to overcome these limitations. Proximity-dependent biotin identification (BioID) is one such widely used PL method. The first-generation BioID enzyme BirA*, a promiscuous bacterial biotin ligase, has been effectively used in cultured mammalian cells; however, relatively slow enzyme kinetics make it less effective for temporal analysis of protein interactions. In addition, BirA* exhibits reduced activity at temperatures below 37°C, further restricting its use in intact organisms cultured at lower optimal growth temperatures ( e.g., Drosophila melanogaster ). TurboID, miniTurbo, and BirA*-G3 are next generation BirA* variants with improved catalytic activity, allowing investigators to use this powerful tool in model systems such as flies. Here, we describe a detailed experimental workflow to efficiently identify the proximal proteome (proximitome) of a protein of interest (POI) in the Drosophila brain using CRISPR/Cas9-induced homology-directed repair (HDR) strategies to endogenously tag the POI with next generation BioID enzymes.

POS0429 ACTIVATED RHEUMATOID ARTHRITIS SYNOVIAL FIBROBLASTS ALTER OSTEOCLAST DIFFERENTIATION AND ACTIVITY

Background

In rheumatoid arthritis (RA), osteoclasts are one of the most important mediators of bone erosion. In addition, RA synovial fibroblasts (RASF) have a major influence on joint erosion in RA. They affect osteoclast differentiation e.g. by increased RANKL production or secretion of other pro-osteoclastogenic factors such as IL-6. In addition to the pro-osteoclastogenic effect of soluble factors such as RANKL and IL-1, visfatin inhibits osteoclast differentiation. Furthermore, visfatin increases the secretion of pro-inflammatory factors by RASF, such as IL-6 or matrix degrading enzymes.

Objectives

In this study, the effect of RASF with/without activation by visfatin and IL-1 on osteoclastogenesis was evaluated.

Methods

Blood from healthy donors and RA patients was used for PBMC isolation. RANKL, TGF-β and hM-CSF were added to induce osteoclast differentiation. RASF-conditioned media (CM) were prepared from confluent RASF cultured for 48h. Differentiating PBMCs in monoculture were compared to PBMC cultured with CM from RASF (CM: 10%, 20%, 30%) as well as in direct co-culture with RASF with/without stimulation with IL-1 (0.05ng/ml), visfatin (25ng/ml). After two weeks in culture, cells were stained using TRAP staining. 3-5 images per well were used for quantification dependent on the variability of the wells. IL-6 was measured by ELISA in supernatants collected at day 14.

Results

IL-6 production increased by IL-1 (e.g. co-culture: 2,8-fold) and visfatin (CM-visfatin: 10%=4,3-fold, 20%=5,4-fold, 30%=4,2-fold; co-culture: 9,5-fold) compared to unstimulated control in all settings. In addition, IL-6 was increased with the addition of CM compared to unstimulated controls (healthy donors CM 30%: unstimulated p=0.0342, IL-1 p=0.0133, visfatin p=0,0133; RA: unstimulated p=0.0133, IL-1 p=0.0342, visfatin p=0.0133, n=3 each). Of note, baseline IL-6 concentrations were higher in PBMC from RA patients compared to healthy donors. Co-culture showed an additional increase in IL-6 levels in all settings (e.g. monoculture: IL-1 4.71±5.75pg/ml, visfatin 141.09±182.79pg/ml; co-culture: IL-1 7241±10398pg/ml, visfatin 24535±16994pg/ml;). During osteoclast differentiation, addition of CM showed similar osteoclastogenesis with similar proportion of osteoclasts with 2 and 3-5 vs. higher numbers of nuclei per cell compared to control. In coculture with RASF osteoclasts showed a stronger TRAP signal compared to monoculture especially for unstimulated and IL-1 stimulated co-cultures.

Conclusion

Both, in monoculture with CM and in coculture, IL-6 levels were increased compared to control, whereas in RA patients the IL-6 levels were higher compared to healthy donors. The CM containing secreted factors of RASF did not have a prominent influence on osteoclastogenesis. However, the presence of RASF increased the TRAP signal showing an increased activity of differentiated osteoclasts especially in unstimulated and IL-1 stimulated co-cultures but not with addition of visfatin.

References

None.

Disclosure of Interests

None declared.

Absolute calibration of Fujifilm BAS-TR image plate response to laser driven protons up to 40 MeV

Image plates (IPs) are a popular detector in the field of laser driven ion acceleration, owing to their high dynamic range and reusability. An absolute calibration of these detectors to laser-driven protons in the routinely produced tens of MeV energy range is, therefore, essential. In this paper, the response of Fujifilm BAS-TR IPs to 1-40 MeV protons is calibrated by employing the detectors in high resolution Thomson parabola spectrometers in conjunction with a CR-39 nuclear track detector to determine absolute proton numbers. While CR-39 was placed in front of the image plate for lower energy protons, it was placed behind the image plate for energies above 10 MeV using suitable metal filters sandwiched between the image plate and CR-39 to select specific energies. The measured response agrees well with previously reported calibrations as well as standard models of IP response, providing, for the first time, an absolute calibration over a large range of proton energies of relevance to current experiments.

Enhancement of the Nonresonant Streaming Instability by Particle Collisions

Streaming cosmic rays can power the exponential growth of a seed magnetic field by exciting a nonresonant instability that feeds on their bulk kinetic energy. By generating the necessary turbulent magnetic field, it is thought to play a key role in the confinement and acceleration of cosmic rays at shocks. In this Letter we present hybrid-particle-in-cell simulations of the nonresonant mode including Monte Carlo collisions, and investigate the interplay between the pressure anisotropies produced by the instability and particle collisions in the background plasma. Simulations of poorly ionized plasmas confirm the rapid damping of the instability by proton-neutral collisions predicted by linear fluid theory calculations. In contrast we find that Coulomb collisions in fully ionized plasmas do not oppose the growth of the magnetic field, but under certain conditions suppress the pressure anisotropies and actually enhance the magnetic field amplification.

Pulsed magnetic field generation system for laser-plasma research

An up to 15 T pulsed magnetic field generator in a volume of a few cubic centimeters has been developed for experiments with magnetized laser plasma. The magnetic field is created by a pair of coils placed in a sealed reservoir with liquid nitrogen, installed in a vacuum chamber with a laser target. The bearing body provides the mechanical strength of the system both in the case of co-directional and oppositely connected coils. The configuration of the housing allows laser radiation to be introduced into the working area between the coils in a wide range of directions and focusing angles, places targets away from the symmetry axis of the magnetic system, and irradiates several targets simultaneously.

In vivo Profiling of the Alk Proximitome in the Developing Drosophila Brain

Anaplastic lymphoma kinase (Alk) is an evolutionary conserved receptor tyrosine kinase belonging to the insulin receptor superfamily. In addition to its well-studied role in cancer, numerous studies have revealed that Alk signaling is associated with a variety of complex traits such as: regulation of growth and metabolism, hibernation, regulation of neurotransmitters, synaptic coupling, axon targeting, decision making, memory formation and learning, alcohol use disorder, as well as steroid hormone metabolism. In this study, we used BioID-based in vivo proximity labeling to identify molecules that interact with Alk in the Drosophila central nervous system (CNS). To do this, we used CRISPR/Cas9 induced homology-directed repair (HDR) to modify the endogenous Alk locus to produce first and next generation Alk::BioID chimeras. This approach allowed identification of Alk proximitomes under physiological conditions and without overexpression. Our results show that the next generation of BioID proteins (TurboID and miniTurbo) outperform the first generation BirA* fusion in terms of labeling speed and efficiency. LC-MS3-based BioID screening of Alk^TurboID and Alk^miniTurbo larval brains revealed an extensive neuronal Alk proximitome identifying numerous potential components of Alk signaling complexes. Validation of Alk proximitome candidates further revealed co-expression of Stardust (Sdt), Discs large 1 (Dlg1), Syntaxin (Syx) and Rugose (Rg) with Alk in the CNS and identified the protein-tyrosine-phosphatase Corkscrew (Csw) as a modulator of Alk signaling.

Design and commissioning of a neutron counter adapted to high-intensity laser matter interactions

The advent of multi-PW laser facilities world-wide opens new opportunities for nuclear physics. With this perspective, we developed a neutron counter taking into account the specifics of a high-intensity laser environment. Using GEANT4 simulations and prototype testings, we report on the design of a modular neutron counter based on boron-10 enriched scintillators and a high-density polyethylene moderator. This detector has been calibrated using a plutonium-beryllium neutron source and commissioned during an actual neutron-producing laser experiment at the LULI2000 facility (France). An overall efficiency of 4.37(59)% has been demonstrated during calibration with a recovery time of a few hundred microseconds after laser-plasma interaction.

Mass Spectrometry Proteotyping-Based Detection and Identification of Staphylococcus aureus, Escherichia coli, and Candida albicans in Blood

Bloodstream infections (BSIs), the presence of microorganisms in blood, are potentially serious conditions that can quickly develop into sepsis and life-threatening situations. When assessing proper treatment, rapid diagnosis is the key; besides clinical judgement performed by attending physicians, supporting microbiological tests typically are performed, often requiring microbial isolation and culturing steps, which increases the time required for confirming positive cases of BSI. The additional waiting time forces physicians to prescribe broad-spectrum antibiotics and empirically based treatments, before determining the precise cause of the disease. Thus, alternative and more rapid cultivation-independent methods are needed to improve clinical diagnostics, supporting prompt and accurate treatment and reducing the development of antibiotic resistance. In this study, a culture-independent workflow for pathogen detection and identification in blood samples was developed, using peptide biomarkers and applying bottom-up proteomics analyses, i.e., so-called "proteotyping". To demonstrate the feasibility of detection of blood infectious pathogens, using proteotyping, Escherichia coli and Staphylococcus aureus were included in the study, as the most prominent bacterial causes of bacteremia and sepsis, as well as Candida albicans, one of the most prominent causes of fungemia. Model systems including spiked negative blood samples, as well as positive blood cultures, without further culturing steps, were investigated. Furthermore, an experiment designed to determine the incubation time needed for correct identification of the infectious pathogens in blood cultures was performed. The results for the spiked negative blood samples showed that proteotyping was 100- to 1,000-fold more sensitive, in comparison with the MALDI-TOF MS-based approach. Furthermore, in the analyses of ten positive blood cultures each of E. coli and S. aureus, both the MALDI-TOF MS-based and proteotyping approaches were successful in the identification of E. coli, although only proteotyping could identify S. aureus correctly in all samples. Compared with the MALDI-TOF MS-based approaches, shotgun proteotyping demonstrated higher sensitivity and accuracy, and required significantly shorter incubation time before detection and identification of the correct pathogen could be accomplished.