A Framework for Quality Control in Quantitative Proteomics.

A thorough evaluation of the quality, reproducibility, and variability of bottom-up proteomics data is necessary at every stage of a workflow, from planning to analysis. We share vignettes applying adaptable quality control (QC) measures to assess sample preparation, system function, and quantitative analysis. System suitability samples are repeatedly measured longitudinally with targeted methods, and we share examples where they are used on three instrument platforms to identify severe system failures and track function over months to years. Internal QCs incorporated at the protein and peptide levels allow our team to assess sample preparation issues and to differentiate system failures from sample-specific issues. External QC samples prepared alongside our experimental samples are used to verify the consistency and quantitative potential of our results during batch correction and normalization before assessing biological phenotypes. We combine these controls with rapid analysis (Skyline), longitudinal QC metrics (AutoQC), and server-based data deposition (PanoramaWeb). We propose that this integrated approach to QC is a useful starting point for groups to facilitate rapid quality control assessment to ensure that valuable instrument time is used to collect the best quality data possible. Data are available on Panorama Public and ProteomeXchange under the identifier PXD051318.

Rapid Screening Evaluation of SARS-CoV-2 IgG Assays Using Z-Scores to Standardize Results.

Many serologic tests are now available for measuring severe acute respiratory syndrome coronavirus 2 antibodies to evaluate potential protective immunity and for seroprevalence studies. We describe an approach to standardizing positivity thresholds and quantitative values for different assays that uses z-scores to enable rapid and efficient comparison of serologic test performance.

JC-virus seroconversion in multiple sclerosis patients receiving natalizumab.

AIM: The objectives of this study were to evaluate the rate of JC virus (JCV) seroconversion/seroreversion in a French cohort of multiple sclerosis (MS) patients receiving natalizumab (NTZ), describe the characteristics of this population, identify risk factors for JCV seropositivity and analyse the additional value of quantitative JCV serology results in this context. METHODS: MS patients from two French MS centres, whose JCV serological status in 2011 while receiving NTZ was known (n=357; first-generation enzyme-linked immunosorbent assay (ELISA) test (Gen1)), were proposed for inclusion in this study. We evaluated the rate of JCV seroconversion over a period of one year with a second-generation ELISA test (Gen2; n=303) and analysed the quantitative results. Multivariate analysis was performed to identify risk factors for JCV seropositivity. RESULTS: Among the patients with Gen2 JCV serology (n=303) that had been JCV-seronegative one year before (n=165), the rate of JCV seroconversion was 26.67% (44/165). We observed a higher proportion of anti-JCV antibody seroconverters (14.5%) than expected (≤3%) but also increasing index values of anti-JCV antibody over time. CONCLUSION: Our data suggest that JCV reactivation occurs during NTZ therapy and leads to an increase in the anti-JCV antibodies titre, thus making them more easily detectable by the second-generation ELISA test.

A framework for quality control in quantitative proteomics.

A thorough evaluation of the quality, reproducibility, and variability of bottom-up proteomics data is necessary at every stage of a workflow from planning to analysis. We share real-world case studies applying adaptable quality control (QC) measures to assess sample preparation, system function, and quantitative analysis. System suitability samples are repeatedly measured longitudinally with targeted methods, and we share examples where they are used on three instrument platforms to identify severe system failures and track function over months to years. Internal QCs incorporated at protein and peptide-level allow our team to assess sample preparation issues and to differentiate system failures from sample-specific issues. External QC samples prepared alongside our experimental samples are used to verify the consistency and quantitative potential of our results during batch correction and normalization before assessing biological phenotypes. We combine these controls with rapid analysis using Skyline, longitudinal QC metrics using AutoQC, and server-based data deposition using PanoramaWeb. We propose that this integrated approach to QC be used as a starting point for groups to facilitate rapid quality control assessment to ensure that valuable instrument time is used to collect the best quality data possible.

Efficiency of five samplers to trap suspended particulate matter and microplastic particles of different sizes.

Suspended particulate matter (SPM) plays a major role in nutrient cycles and for the transport of pollutants within local and transboundary water catchments. Obtaining representative SPM samples from rivers, lakes, inland and coastal waters is crucial for quantitative and qualitative chemical analyses to correctly describe the chemical status of a water body. However, a representative sampling of SPM over time is challenging due to the heterogeneity of SPM particles sizes, their non-uniform distribution in rivers, and a variety of sampling devices being in use. Therefore, we investigated the efficiencies of five different sampling devices commonly used in national and international monitoring programs to collect representative SPM samples. We tested three passive sedimentation-based samplers (SBSs: sedimentation box, SB; sedimentation tank, ST; Raetz Sampler, RS), and two active separation techniques (continuous flow centrifuge, CFC; vacuum filtration, VF) in an experimental laboratory setup using in-house SPM standard suspensions (mineral, organic, and microplastic particles) with defined particle sizes. The mass-based efficiencies of the three examined SBSs were 0-66% for the mineral and organic particles <75 µm, where the mean particle sizes of collected samples were always shifted to bigger sizes compared to the initial suspensions. The efficiencies of the three SBSs to collect microplastic particles <80 µm were <20% due to the lower densities of microplastic compared to organic and mineral particles. In contrast to the SBSs, VF and CFC units showed excellent efficiencies >86% for all tested materials, with similar particle size distributions of the sampled material compared to those of the inlet suspensions. In conclusion, SPM sampling efficiencies of sampling units have to be carefully considered and compared to the respective aims of the monitoring approaches, especially when statements are derived from quantitative results on SPM.

An evaluation of measurement uncertainty of trajectory angles using a 3D laser scanner.

Measuring trajectory angles of bullet defects at a crime scene is an important part of crime scene investigation as these angles can be used for shooting incident reconstructions. The Washington State Patrol Crime Scene Response Team (WSP CSRT) had a desire to report and use measured trajectory angles. To report quantitative measurements, a statement of uncertainty for the measurement must also be reported due to an accreditation requirement through the ANSI National Accreditation Board (ANAB), through which the WSP CSRT is accredited. This evaluation examined the measurement uncertainty of the 3D laser scanning method that the WSP CSRT utilizes for measuring the vertical and azimuth angles from trajectory rods fitted to bullet defects. Three studies were performed which examined the variation of vertical and azimuth angle measurements from trajectory rods on flat surfaces, the variation of azimuth angle measurements from a trajectory rod on a curved surface, and a traceability study with known vertical and azimuth angle measurements. Seven common substrates were selected as target materials and were shot with 9 mm Luger and 0.45 Auto caliber bullets. A vehicle with one bullet defect was utilized for the curved surface study. The WSP's current fleet of Trimble X7 3D laser scanners, the WSP Criminal Investigation Division (CID) Detectives who operate these scanners, and the Forensic Scientists responsible for trajectory rod placement and angle measurements were utilized. An overall measurement uncertainty of +/- 2.6 degrees at an approximate 95% confidence interval was determined for all trajectory angles measured from trajectory rods.

Mediumship accuracy: A quantitative and qualitative study with a triple-blind protocol.

AIMS: assess if mediums could give accurate information about the deceased in a triple-blind protocol and to investigate the source of information using a quantitative and qualitative analysis. METHODS: nine mediums produced thirty-eight readings related to thirty-eight deceased individuals chosen by thirty-six sitters using a triple-blind protocol with no direct interaction with the sitters themselves. In this protocol, the medium was provided with only the deceased's name by the interviewer, the latter having no further knowledge about the deceased. In every session, the medium was asked to provide information about two deceased persons of the same gender. This information, excluding generic details, was entered into two anonymous lists. The information of these two readings was sent to the research assistant charged with maintaining contact with the sitters. Each sitter was asked to assign a value to every piece of information listed using a four- point Likert scale from 'totally wrong' to 'totally correct', and to provide a global score for each reading. RESULTS: 65.8% of the intended readings were correctly identified with respect to the chance of 50%. Furthermore, intended readings had on average 29.5% more correct information than the control ones. Qualitative data indicate that mediums attain information both passively and actively, that is as if they retrieved information without or directly interacting with the deceased. CONCLUSIONS: this study provides further evidence that some mediums are able to obtain accurate information about deceased people knowing only the deceased's name and with no interaction with sitters; it also supports the hypothesis that, in some cases, the sources of the information are the deceased themselves.

Rapid multiplex PCR assays in patients with respiratory viral infections: is semi-quantitative data useful? A pilot study.

Viral respiratory rapid multiplex PCR assays FilmArray® (FA) and ePlex® (eP) provide qualitative results which may not reflect clinical relevance. In a pilot study, we report retrospectively whether the semi-quantitative PCR assay R-GENE® would have facilitated clinical interpretation. Forty-four patients were hospitalized for various respiratory manifestations; all of them have benefited from a respiratory sample during acute symptoms. Among the 44 patients, FA detected 23 positive samples including 31 viruses, 26 of them gave high or moderate R-GENE® scores (cycle threshold < 35), and all but one were consistent with clinical history. Semi-quantitative scores would have allowed for critical interpretation of the results; those are a key additional element for an optimal exploitation of the rapid multiplex PCR assays power.

Resolving embarrassing medical conditions with online health information.

PURPOSE: Reliance on online health information is proliferating and the Internet has the potential to revolutionize the provision of public health information. The anonymity of online health information may be particularly appealing to people seeking advice on 'embarrassing' health problems. The purpose of this study was to investigate (1) whether data generated by the embarrassingproblems.com health information site showed any temporal patterns in problem resolution, and (2) whether successful resolution of a medical problem using online information varied with the type of medical problem. METHODS: We analyzed the responses of visitors to the embarrassingproblems.com website on the resolution of their problems. The dataset comprised 100,561 responses to information provided on 77 different embarrassing problems grouped into 9 classes of medical problem over an 82-month period. Data were analyzed with a Bernoulli Generalized Linear Model using Bayesian inference. RESULTS: We detected a statistically important interaction between embarrassing problem type and the time period in which data were collected, with an improvement in problem resolution over time for all of the classes of medical problem on the website but with a lower rate of increase in resolution for urinary health problems and medical problems associated with the mouth and face. As far as we are aware, this is the first analysis of data of this nature. CONCLUSIONS: Findings support the growing recognition that online health information can contribute to the resolution of embarrassing medical problems, but demonstrate that outcomes may vary with medical problem type. The results indicate that building data collection into online information provision can help to refine and focus health information for online users.