Dedicated Software Tool Research Articles

Mobile Workflow in Computed Tomography of the Chest

A CT system with a tablet as mobile user interface and a wireless remote control for positioning and radiation release has recently been presented. Our aim was to evaluate the effects of a mobile CT examination workflow on the radiographers’ performance compared to conventional examinations. A prototype of a radiation protection cabin was installed besides the gantry of a CT system. The CT system was equipped with a simplified user interface on a portable tablet and a mobile remote control. 98 patients with an indication for CT of the chest were randomly assigned to examination using the mobile devices (study group, n = 47) or using the conventional stationary workflow on the console (reference group, n = 51). Three ceiling mounted fisheye cameras were used for motion tracking of the radiographers, two in the examination room and one in the control room. Relative density of detection heat-maps and area counts were assessed using a dedicated software tool to quantify radiographers’ movements. Duration of each task of the examination was manually recorded using a stopwatch. In the reference group 25% of the area counts were located inside of the examination room, while it was 48% in the study group. The time spent in the same room with the patient increased from 3:06 min (29%) to 6:01 min (57%) using the mobile workflow (p < 0.05), thereof 0:59 min (9%) were spent in moderate separation with maintained voice and visual contact in the radiation protection cabin. Heat-maps showed an increase of the radiographer’s working area, indicating a higher freedom of movement. Total duration of the examination was slightly less in the study group without statistical significance (median time: study 10:36, reference 10:50 min; p = 0.29). A mobile CT examination transfers the radiographers’ interaction with the scanner from the control room into the examination room. There, radiographers’ freedom of movement is higher, without any tradeoffs regarding the examination duration.

LONG-TERM HEALTH RISK AFTER BREAST-CANCER RADIOTHERAPY: OVERVIEW OF PASSOS METHODOLOGY AND SOFTWARE.

Breast-cancer radiotherapy reduces the recurrence rates and improves patient survival. However, it also increases the incidence of second cancers and of heart disease. These radiation-induced long-term health risks become increasingly important with improved cure rates and prolonged patient survival. Radiation doses to nearby as well as distant organs strongly vary between different irradiation techniques and among individual patients. To provide personalized lifetime risk estimates, the German national project PASSOS combines individual anatomy, dosimetric estimates, organ-specific low- and high-dose risk models and personal risk factors such as smoking. A dedicated software tool is under development to assist clinical decision-making processes.

Application of Artificial Neural Networks in the Dimensioning of Retention Reservoirs

Abstract One of the essential needs for retention reservoirs is to reduce the volume of wastewater flows in sewer systems. Their main advantage is the potential to increase retention in the system, which in turn improves hydraulic safety by reducing the risk of node flooding and the emergence of the phenomenon of “urban flooding”. The increasingly common use of retention reservoirs, the observed changes in the climate and the development of dedicated software tools necessitate the updating of the methods used to dimension retention reservoirs. So far, the best known procedures in this regard involve the application of analytical formulas and tools in the hydrodynamic modelling of current sewage systems. In each case the basis for the retention facility design is the evaluation of rainfall in terms of the probability of occurrence and duration that would result in a critical rainwater flow condition in the sewer system in order to define the required reservoir retention capacity. The purpose of this paper is to analyse of the feasibility of applying artificial neural networks in the preliminary estimation of the duration of critical rainfalls. Such an application of these networks is essential to the process of hydrodynamic modelling of the system and to determining the required retention capacity of the reservoir. The study used an artificial neural network model typically used as part of planning processes, as well as the Statistica software suite.

Investigating the perception of soundscapes through acoustic scene simulation.

This paper introduces a new experimental protocol for studying mental representations of urban soundscapes through a simulation process. Subjects are asked to create a full soundscape by means of a dedicated software tool, coupled with a structured sound data set. This paradigm is used to characterize urban sound environment representations by analyzing the sound classes that were used to simulate the auditory scenes. A rating experiment of the soundscape pleasantness using a seven-point bipolar semantic scale is conducted to further refine the analysis of the simulated urban acoustic scenes. Results show that (1) a semantic characterization in terms of presence/absence of sound sources is an effective way to characterize urban soundscape pleasantness, and (2) acoustic pressure levels computed for specific sound sources better characterize the appraisal than the acoustic pressure level computed over the overall soundscape.

Ultra-low-dose limited renal CT for volumetric stone surveillance: advantages over standard unenhanced CT.

To describe and validate a novel CT approach using volumetric analysis for renal stone surveillance. This prospective trial consisted of a standard low-dose non-contrast CT (SLD) of the abdomen and pelvis, immediately followed by an ultra-low-dose non-contrast CT (ULD) with reconstruction limited to the kidneys. A novel dedicated software tool was applied that automates stone volume, density, and maximum linear size. Manual linear stone size was measured by a radiology fellow and urology resident for comparison. CT dose and clinical charges were considered. Twenty-eight stones in 16 patients were analyzed. Mean effective dose of ULD CT was 0.57mSv, an average 92% lower than the SLD CT dose. For SLD, mean size ± SD (range) (mm) was 7.9 ± 6.2 (2.6-30.5) for Reader 1, 7.3 ± 6 (2.4-30.7) for Reader 2, and 9.3 ± 6.4 (3.7-33.1) for the automated software. For ULD, mean size ± SD (range) (mm) was 7.3 ± 6 (2.5-30.5) for Reader 1, 7.2 ± 6.1 (2.1-30.7) for Reader 2, and 9.1 ± 6.4 (4.2-32.8) for the automated software. Automated stone diameters were larger than manual diameters for 27/28 stones (mean difference, 23%); difference was ≥ 2mm in 30%. Average variability between manual measurements was 8.6% (SLD) and 7.8% (ULD), but was 0% for the automated technique. Our institutional charge for ULD renal CT is slightly less than renal US, and > 4× less than SLD CT. The Medicare global fee for the ULD renal CT is less than the SLD CT of the abdomen and pelvis. This focused stone surveillance CT protocol is lower cost and lower dose compared to the standard CT approach. Automated assessment of stone burden provides improved reproducibility over manual linear measurement and offers the advantages of 3D measurements and volumetry. We now offer and perform this protocol in routine clinical practice for stone surveillance.

OA216] Development of breast tumours models database

Purpose We present the development and the current state of the MaXIMA Breast Tumours Models’ Database, which is intended to provide researchers with both segmented and mathematically modelled realistic in shape computer-based breast tumours. Methods The database contains various 3D images of breast cancers of irregular shapes, collected from routine patient examinations or dedicated scientific experiments. It also contains images of simulated tumour models. To extract the 3D shapes of the breast cancers from patient images, an in–house developed and well evaluated segmentation algorithm was applied on 60 tomosynthesis sets from patients diagnosed with malignant and benign lesions. In addition, three breast mastectomy cases scanned at a CT system were added. This algorithm includes a series of image processing operations and region-growing techniques with minimal interaction from the user to find and segment the areas of the lesions. Modelled computational breast tumours are generated following different approaches and also stored in the database. Each record in the database is supported with relevant information, e.g. voxel size and resolution, matrix size, geometrical centre, etc. Results The MaXIMA Imaging Database currently contains 68 unique breast cancer models obtained by segmentation of 3D patient breast tomosynthesis images; 8 models obtained by segmentation of 3D micro CT images of biopsy specimens; and 20 models based on mathematical algorithm. An application of the tumour models is to insert them into computationally generated healthy breast phantom generated with dedicated software tools (e.g. the BreastSimulator tool). The resulted combined computational breast models are used to study the visibility of breast tumours in 3D breast imaging techniques. This approach allows implementation of multiple scenarios and unlimited number of cases, which can be used for further software modelling and investigation of breast imaging techniques. The database interface is web-based, i.e. is platform independent, user friendly and is indented to be made freely accessible through internet after the completion of the MaXIMA project. Conclusions The developed database serves as an imaging data source for researchers, working on breast imaging and early breast cancer detection with the help of existing or newly developed imaging modalities.

P068] Management of clinical MRI workflow and gadolinium dosing using a dedicated software tool

Purpose To ensure the place of MRI in the future of value-based healthcare, patient safety and cost-efficiency needs to be increased. It has been shown in other imaging modalities, that accessible management software-tools provide insights into everyday workflow, and facilitate optimization of practices [1] . In this study, we demonstrate the added value of such software in a clinical MRI setting. Methods DICOM data from 3 months was automatically collected from 3 Siemens MR systems (1.5T, two 3T) on a server, using software from GE Healthcare. Operational and clinical data (procedure- and sequence-timing, gadolinium contrast agents (GDCA) volume, etc.) was extracted in excel-format. Descriptive statistics of MRI workflow were generated, and the administration of GDCA was compared to standards [2] . Results Data from 3409 MRI procedures was collected; 2733 (80,2%) were performed without GDCA, 659 (19,3%) and 1 ( [1] . In only 0,4% of GDCA enhanced procedures the maximum allowed injected volume was exceeded. However, in 56,4% of cases the injected volume was larger than the guideline [2] prescribes, indicating optimization possibilities. When excluding overnight stops, between-patient time was significantly different between one of the 3T scanners and the 1.5T scanner (averages 14m34s and 16m6s; t-test p-value = 0,006). Opportunities for optimizing patient-throughput are to be investigated; minimizing between-patient time can increase cost-efficiency. Conclusions Easy data-access on GDCA administration is of interest because of recent concerns about their safety [3] . Volume of GDCA can be readily tracked and optimized using this software, showing its contribution to patient safety. Additionally, between-patient time can be monitored and minimized to increase cost-efficiency. Future work will be focused on further development of features for patient safety (SAR levels, contrast allergies, implant safety).

Dynamic coronary roadmapping during percutaneous coronary intervention: a feasibility study

BackgroundA novel software (“Dynamic Coronary Roadmap”) was developed, which offers a real-time, dynamic overlay of the coronary tree on fluoroscopy. Once the roadmap has been automatically generated during angiography it can be used for navigation during percutaneous coronary interventions (PCI). As a feasibility study, we aimed to investigate the feasibility of real-time dynamic coronary roadmapping and consecutive coronary overlay during elective PCI.Methods and resultsWe studied 936 overlay runs, created following the same amount of angiographies, which were generated during 36 PCIs. Feasibility of dynamic coronary roadmapping was analyzed using a dedicated software tool. Roadmap quality (correct dynamic imaging of the vessels without relevant artefacts or missing parts) was distinguished from overlay quality (congruence of dynamic coronary roadmapping and coronary anatomy). Additionally, we assessed procedural success and the occurrence of major cardiac and cerebrovascular events (MACCE). Roadmap quality was defined as “fit for use” in 99.5%. In 97.4% of runs overlay quality was deemed “fit for use”. Overall, we observed low inter and intra observer variability (ICC R = 0.84 for roadmap quality and R = 0.75 for overlay quality). Procedural success rate was 100%. MACCE occurred in two (5.6%) patients during post-interventional in-hospital stay and were not software-related.ConclusionsDynamic coronary roadmapping provides in > 98% of cases sufficient roadmap quality with an anatomically correct overlay of the coronary vessels with good inter and intra observer variability. Future randomized studies are warranted to test possible advantages like procedure time reduction and less consumption of contrast medium.

MAOS - Oxygen Minimum Amount Calculation Software for Thermodynamics Processes

The present paper aims to exhibit a dedicated software tool (MAOS) which determine the amount of fresh air introduced into each cylinder for 2 and 4-stroke naval engines, taking into account the current "Fuel-Efficient and Non-Polluting Engines" trends. The quantity of air, known as ‘fresh load’, determines the quality of the fuel’s oil oxidation processes and the heat transfer inside the piston’s head. Thus, in order to maintaining the oxidation process, the software determine the active component in the fresh load, represented by the oxygen and the excess of air, known as alpha. The software comes to the attention of young naval engineers as a validating current computing techniques precursor, using existing theoretical methods.

1D portable optical coherence tomography system

Imaging methods are an expanding branch of technology, which involves data acquisition and analysis of images for research and diagnostics. This paper has been devoted to describe the optical design for one-dimensional, portable optical coherence tomography (OCT) system. The Mach-Zehnder interferometer has been designed in the presented study. Description of the construction and applied hardware solutions have been written. Moreover, a dedicated software tools for signal processing and data acquisition have been developed Full Text: PDF ReferencesStrąkowski, M. R., Pluciński, J., Jędrzejewska-Szczerska, M., Hypszer, R., Maciejewski, M., Kosmowski, B. B., "Polarization sensitive optical coherence tomography for technical materials investigation", Sensors and Actuators A: Physical 142(1), 104-110 (2008). CrossRef J. G. Fujimoto, W. Drexler, Optical Coherence Tomography: Technology and Applications (Biological and Medical Physics, Biomedical Engineering), (New York, Springer 2008). CrossRef Mujat, M., Chan, R. C., Cense, B., Park, B. H., Joo, C., Akkin, T., De Boer, J. F., "Retinal nerve fiber layer thickness map determined from optical coherence tomography images", Opt. Express 13, 9480-9491 (2005). CrossRef Liang, H., Cid, M. G., Cucu, R. G., Dobre, G. M., Podoleanu, A. G., Pedro, J., Saunders, D., "En-face optical coherence tomography-a novel application of non-invasive imaging to art conservation", Opt. Express 13, 6133-6144 (2005). CrossRef Choma, M. A., Sarunic, M. V., Yang, C., Izatt, J. A., "Sensitivity advantage of swept source and Fourier domain optical coherence tomography", Opt. Express 11, 2183-2189 (2003). CrossRef Koyama, T., Marshek, K. M., "Toothed belt drives—past, present and future", Mechanism and machine theory 23(3), 227-241 (1988). CrossRef Ali, M., &amp; Parlapalli, R., "Signal processing overview of optical coherence tomography systems for medical imaging", Texas Instruments, SPRABB9–June (2010). DirectLink B. E. A. Saleh, M. C. Teich, Fundamentals of Photonics, 2nd Edition (New York, Wiley 1991) CrossRef

Group decision-making in software architecture: A study on industrial practices

ContextA Software Architecture results from a comprehensive process in which several stakeholders deliberate upon the key requirements, issues, solutions and make architectural design decisions. Literature shows that most architectural decisions, in practice, are made in groups. Still, there is a limited understanding of industrial group decision-making practices in software architecture and the challenges that software architecture groups face. ObjectiveOur study, by drawing inspiration from group decision-making theories and models, aims at understanding (i) Existing decision-making practices in software architecture groups (ii) the comparison between practice and theory, (iii) the challenges that the groups face, and (iv) the satisfaction of group members with various aspects of Group Decision Making. MethodThe study has been conducted through a questionnaire-based survey. 35 practitioners participated in this survey and the responses were analyzed qualitative and quantitatively. ResultsThe analysis of individual responses reveal that software architecture groups (composed, on average, of 3–5 co-located or dispersed members) adopt a discussion based approach while evaluating alternatives, thereby lacking a structured way of decision-making. In these groups, despite the involvement of group members in the discussions, the final decision is made by an individual of authority. Not only is structured decision-making less common, the usage of dedicated software tools for decision-making too is rare. These groups face challenges that are indicative of Groupthink and Group Polarization. Group members feel that quantity of alternatives generated during discussions and tool availability are below satisfactory and they have low satisfaction with the tool support available. ConclusionThis study has helped us develop an understanding of software architecture groups, their decision-making practices and challenges faced together with the satisfaction of group members. What the industry needs is integration of group decision-making principles into software architecture decision-making and design of decision-making tools that assist the architecture groups.

An efficient human whole blood workflow using CyTOF technology: a lyophilized 30-plex antibody panel coupled with automated data analysis

Abstract CyTOF® mass cytometry is a highly multiplexed, single-cell analysis platform that uses metal-tagged antibodies. A significant advantage of this technology is its ability to resolve more than 30 markers in a single panel without the need for compensation. Nonetheless, a highly multiplexed panel requires optimization of antibody titers, full panel verification, sample preparation, data acquisition, and analysis. Preparation of a staining cocktail from 30 individual tubes may be prone to errors. Not only is data analysis time-consuming for complex panels, it is difficult to interpret without expertise in immunology. We have developed a lyophilized 30-plex immunphenotyping panel contained in a single tube, an efficient workflow, and an automated software solution for human whole blood analysis using mass cytometry. The panel focuses on T cell lineage while also capturing other relevant immune populations. Blood is added directly to the lyophilized antibody tube, followed by RBC lysis, wash, and fixation steps and finally data acquisition of stained samples on the Helios™ system. The dedicated software tool accepts FCS3.0 files and in under 10 minutes automatically generates reports on the number of live cells, percentage of specific cell populations, staining intensities, histograms, 2D dot plots, and tSNE graphs. The auto-calculated frequencies of populations are comparable to manual gating, with a validated correlation coefficient over 0.9. The panel and software tool enable researchers to streamline immunophenotyping of whole blood while accurately and reproducibly monitoring changes in immune cell subsets in patient samples.

Computation and analysis of the extremely low frequency electric and magnetic fields generated by two designs of 400 kV overhead transmission lines

The overhead transmission lines are considered one of the major sources of electric and magnetic fields, which can induce electrical currents within the human body. In this study, the electric and magnetic fields generated by two recent designs of 400 kV transmission lines used in the Romanian power system are computed and compared to the exposure limits established by the International Commission on Non-Ionizing Radiation Protection for the general public. The computations are carried out with two dedicated software tools, called PowerMag and PowerELT, which have been developed based on a 2D quasi-static analytical approach. This approach, as well as the electric and magnetic field distributions obtained for the considered 400 kV overhead transmission lines, will be discussed in detail. To confirm the validity of the results, some comparisons to finite element computations will also be presented.

Dose Reduction and Dose Management in Computed Tomography - State of the Art.

For years, the number of performed CT examinations has been rising. At the same time, computed tomography became more dose efficient. The aim of this article is to give an overview about the state of the art in dose reduction in CT and to highlight currently available tools in dose management. By performing a literature research on Pubmed regarding dose reduction in CT, relevant articles were identified and analyzed. Technical innovations with individual adaptation of tube current and voltage as well as iterative image reconstruction enable a considerable dose reduction with preserved image quality. At the same time, dedicated software tools are able to handle huge amounts of data and allow to optimize existing examination protocols. · CT examinations are increasingly performed and contribute considerably to non-natural radiation exposure.. · A correct indication is crucial for each CT examination.. · The examination protocol has to be tailored to the medical question and patient.. · Multiple technical innovations enable considerable dose reduction with constant image quality.. · Dose management with dedicated software tools gains importance.. · Zinsser D, Marcus R, Othman AE et al. Dose reduction and dose management in computed tomography - State of the art. Fortschr Röntgenstr 2018; 190: 531 - 541.

Chemical crosslinking and mass spectrometry to elucidate the topology of integral membrane proteins.

Here we made an attempt to obtain partial structural information on the topology of multispan integral membrane proteins of yeast by isolating organellar membranes, removing peripheral membrane proteins at pH 11.5 and introducing chemical crosslinks between vicinal amino acids either using homo- or hetero-bifunctional crosslinkers. Proteins were digested with specific proteases and the products analysed by mass spectrometry. Dedicated software tools were used together with filtering steps optimized to remove false positive crosslinks. In proteins of known structure, crosslinks were found only between loops residing on the same side of the membrane. As may be expected, crosslinks were mainly found in very abundant proteins. Our approach seems to hold to promise to yield low resolution topological information for naturally very abundant or strongly overexpressed proteins with relatively little effort. Here, we report novel XL-MS-based topology data for 17 integral membrane proteins (Akr1p, Fks1p, Gas1p, Ggc1p, Gpt2p, Ifa38p, Ist2p, Lag1p, Pet9p, Pma1p, Por1p, Sct1p, Sec61p, Slc1p, Spf1p, Vph1p, Ybt1p).

E-learning for textile enterprises innovation improvement

The Erasmus Plus project- TEXMatrix: “Matrix of knowledge for innovation and competitiveness in textile enterprises”, financed through the Erasmus+ Programme, Strategic partnerships– KA2 for Vocational Education and Training, aims at spreading the creative and innovative organizational culture inside textile enterprises by transferring and implementing methodologies, tools and concepts for improved training. Five European partners form the project consortium: INCDTP – Bucharest, Romania (coordinator), TecMinho - Portugal, Centrocot - Italy, University Maribor, Slovenia, and “Gheorghe Asachi” Technical University of Iasi, Romania. These will help the textile enterprises involved in the project, to learn how to apply creative thinking in their organizations and how to develop the capacity for innovation and change. The project aims to bridge the gap between textile enterprises need for qualified personnel and the young workforce. It develops an innovative knowledge matrix for the tangible and intangible assets of an enterprise and a benchmarking study, based on which a dedicated software tool will be created. This software tool will aid the decision-making enterprise staff (managers, HR specialists, professionals) as well as the trainees (young employees, students, and scholars) to cope with the new challenges of innovation and competitiveness for the textile field. The purpose of this paper is to present the main objectives and achievements of the project, according to its declared goals, with the focus on the presentation of the knowledge matrix of innovation, which is a powerful instrument for the quantification of the intangible assets of textile enterprises.

NmsBuilder: Freeware to create subject-specific musculoskeletal models for OpenSim

Background and objectiveMusculoskeletal modeling and simulations of movement have been increasingly used in orthopedic and neurological scenarios, with increased attention to subject-specific applications. In general, musculoskeletal modeling applications have been facilitated by the development of dedicated software tools; however, subject-specific studies have been limited also by time-consuming modeling workflows and high skilled expertise required. In addition, no reference tools exist to standardize the process of musculoskeletal model creation and make it more efficient. Here we present a freely available software application, nmsBuilder 2.0, to create musculoskeletal models in the file format of OpenSim, a widely-used open-source platform for musculoskeletal modeling and simulation. nmsBuilder 2.0 is the result of a major refactoring of a previous implementation that moved a first step toward an efficient workflow for subject-specific model creation. MethodsnmsBuilder includes a graphical user interface that provides access to all functionalities, based on a framework for computer-aided medicine written in C++. The operations implemented can be used in a workflow to create OpenSim musculoskeletal models from 3D surfaces. A first step includes data processing to create supporting objects necessary to create models, e.g. surfaces, anatomical landmarks, reference systems; and a second step includes the creation of OpenSim objects, e.g. bodies, joints, muscles, and the corresponding model. ResultsWe present a case study using nmsBuilder 2.0: the creation of an MRI-based musculoskeletal model of the lower limb. The model included four rigid bodies, five degrees of freedom and 43 musculotendon actuators, and was created from 3D surfaces of the segmented images of a healthy subject through the modeling workflow implemented in the software application. ConclusionsWe have presented nmsBuilder 2.0 for the creation of musculoskeletal OpenSim models from image-based data, and made it freely available via nmsbuilder.org. This application provides an efficient workflow for model creation and helps standardize the process. We hope this would help promote personalized applications in musculoskeletal biomechanics, including larger sample size studies, and might also represent a basis for future developments for specific applications.

The use of optical coherence tomography for the evaluation of textural changes of grapes exposed to pulsed electric field

Application of pulsed electric fields (PEF) to food is a nonthermal technology of food processing. The short pulses of high intensity electric field can modify the internal structures of fruits and vegetables by affecting the cell permeability. In the presented study three popular grape wine cultivars – Johanniter, Hibernal and Marechal Foch were exposed to PEF at electric field strengths of 3.3kV/cm and 5kV/cm. The significant textural changes of near peel grape layers influenced by electric field were observed in optical coherence tomography (OCT) images, using infrared light of 1300nm. These changes were expressed by the variation of entropy, standard deviation or lacunarity features and evaluated in a dedicated software tool developed by the authors in Matlab environment. The OCT is a non-destructive technique in which no sample preparation is needed and grapes still remain intact (undamaged) during imaging. The OCT cross-sections revealed the progressive process of expanding zone with strong echo in sub-peel layers what may indicate cell permeabilization or even loosing parenchyma cells integrity. Also grape surface deformations under PEF were quantified. It has been shown that the values of considered textural features in near peel grape tissue were related to the intensity of electric field. Marechal Foch cultivar appeared to be more resistant to PEF than two other grape varieties.

Towards dedicated software tools to assist the creation of Virtual Exhibits

As consequence of the technology expansion of recent years, people are nowadays seeking digital interactive experiences. Museums need to understand and embrace this change by creating digital interactive exhibitions that are culturally guaranteed by the institution authority and, at the same time, can be more appealing for the general public. Amongst the new softwares available to this purpose, 3D engines are some of the hardest to handle for people not coming from the Information Technology field, creating a technological gap between the museological space and the third-millennium public’s expectations that results in a lower lever of enjoyment for the public. With the support of Unity3D, one of the most famous and reliable VR-ready 3D engines, a suite of tools called Muse-Tools was developed to reduce this gap by extending the engine’s editor functionalities to provide museums curators with enough tools to plan both real and virtual exhibitions without relying on expert programmers or artists.

To Be or Not to Be? Five Guidelines to Avoid Misassignments in Cross-Linking/Mass Spectrometry.

The number of publications in the field of chemical cross-linking/mass spectrometry (MS) for deriving protein 3D structures and for probing protein/protein interactions has largely increased during the last years. MS analysis of the large cross-linking data sets requires an automated data analysis by dedicated software tools, but applying scoring procedures with statistical methods does not eliminate the fundamental problems of a misassignment of cross-linked products. In fact, we have observed a significant rate of misassigned cross-links in a number of publications, mainly due to the presence of isobaric cross-linked species, an incomplete fragmentation of cross-linked products, and low-mass accuracy fragment ion data. These false assignments will eventually lead to wrong conclusions on the structural information derived from chemical cross-linking/MS experiments. In this contribution, we examine the most common sources for misassigning cross-linked products. We propose and discuss rational criteria and suggest five guidelines that might be followed for a reliable and unambiguous identification of cross-links, independent of the software used for data analysis. In the interest of the cross-linking/MS approach, it should be ensured that only high-quality data enter the structural biology literature. Clearly, there is an urgent need to define common standards for data analysis and reporting formats of cross-linked products.