Dataset Information

RawBeans: A Simple, Vendor-Independent, Raw-Data Quality-Control Tool.

ABSTRACT: Every laboratory performing mass-spectrometry-based proteomics strives to generate high-quality data. Among the many factors that impact the outcome of any experiment in proteomics is the LC-MS system performance, which should be monitored within each specific experiment and also long term. This process is termed quality control (QC). We present an easy-to-use tool that rapidly produces a visual, HTML-based report that includes the key parameters needed to monitor the LC-MS system performance, with a focus on monitoring the performance within an experiment. The tool, named RawBeans, generates a report for individual files or for a set of samples from a whole experiment. We anticipate that it will help proteomics users and experts evaluate raw data quality independent of data processing. The tool is available at https://bitbucket.org/incpm/prot-qc/downloads. The mass-spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the data set identifier PXD022816.

SUBMITTER: Morgenstern D

PROVIDER: S-EPMC8041395 | biostudies-literature | 2021 Apr

REPOSITORIES: biostudies-literature

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RawBeans: A Simple, Vendor-Independent, Raw-Data Quality-Control Tool.

Morgenstern David D Barzilay Rotem R Levin Yishai Y

Journal of proteome research 20210303 4

Every laboratory performing mass-spectrometry-based proteomics strives to generate high-quality data. Among the many factors that impact the outcome of any experiment in proteomics is the LC-MS system performance, which should be monitored within each specific experiment and also long term. This process is termed quality control (QC). We present an easy-to-use tool that rapidly produces a visual, HTML-based report that includes the key parameters needed to monitor the LC-MS system performance, w ...[more]

PMID: 33657803

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Project description:BackgroundTwo-dimensional speckle-tracking echocardiography (2D-STE) enables objective assessment of left atrial (LA) deformation through the analysis of myocardial strain, which can be measured by different speckle-tracking software. The aim of this study was to compare the consistency of 3 different commercially available software, which include vendor-specific software for measuring left ventricle (VSSLV), vendor-independent software packages for measuring LV strain (VISLV) and vendor-independent software packages for measuring LA strain (VISLA).MethodsSixty-four subjects (mean age: 44 ± 16 years, 50% males) underwent conventional echocardiograms using a GE Vivid 9 (GE Ultrasound, Horten, Norway) cardiac ultrasound system. Standard apical 4 and 2 chamber views of the left atrium were obtained in each subject with a frame-rate range of 40-71 frames/s. LA strain during the contraction phase (Sct), conduit phase (Scd), reservoir phase (Sr = Sct + Scd) were analyzed by 2 independent observers and 3 different software.ResultsSct, Scd, Sr were, respectively, - 11.26 ± 2.45%, - 16.77 ± 7.06%, and 28.03 ± 7.58% with VSSLV, - 14.77 ± 3.59%, - 23.17 ± 10.33%, and 38.23 ± 10.99% with VISLV, and - 14.80 ± 3.88%, - 23.94 ± 10.48%, and 38.73 ± 11.56% when VISLA was used. A comparison of strain measurements between VSSLV and VIS (VISLV and VISLA) showed VIS had significantly smaller mean differences and narrower limits of agreement. Similar results were observed in the coefficient of variation (CV) for measurements between VSSLV and VIS (VISLV and VISLA). Comparison of the intra-class correlation coefficients (ICCs) indicated that measurement reliability was weaker with VSSLV (ICC < 0.6) than with VIS (VISLV and VISLA) (ICC > 0.9). For intra-observer ICCs, VISLA > VSSLV = VISLV. For inter-observer ICCs, VSSLV > VISLA > VISLV.ConclusionsSoftware measurement results of LA strain vary considerably. We recommended not measuring LA strain across vendor platforms.

Project description:PurposeThere is an increasing availability of large imaging cohorts [such as through The Cancer Imaging Archive (TCIA)] for computational model development and imaging research. To ensure development of generalizable computerized models, there is a need to quickly determine relative quality differences in these cohorts, especially when considering MRI datasets which can exhibit wide variations in image appearance. The purpose of this study is to present a quantitative quality control tool, MRQy, to help interrogate MR imaging datasets for: (a) site- or scanner-specific variations in image resolution or image contrast, and (b) imaging artifacts such as noise or inhomogeneity; which need correction prior to model development.MethodsUnlike existing imaging quality control tools, MRQy has been generalized to work with images from any body region to efficiently extract a series of quality measures (e.g., noise ratios, variation metrics) and MR image metadata (e.g., voxel resolution and image dimensions). MRQy also offers a specialized HTML5-based front-end designed for real-time filtering and trend visualization of quality measures.ResultsMRQy was used to evaluate (a) n = 133 brain MRIs from TCIA (7 sites) and (b) n = 104 rectal MRIs (3 local sites). MRQy measures revealed significant site-specific variations in both cohorts, indicating potential batch effects. Before processing, MRQy measures could be used to identify each of the seven sites within the TCIA cohort with 87.5%, 86.4%, 90%, 93%, 90%, 60%, and 92.9% accuracy and the three sites within the rectal cohort with 91%, 82.8%, and 88.9% accuracy using unsupervised clustering. After processing, none of the sites could be distinctively clustered via MRQy measures in either cohort; suggesting that batch effects had been largely accounted for. Marked differences in specific MRQy measures were also able to identify outlier MRI datasets that needed to be corrected for common acquisition artifacts.ConclusionsMRQy is designed to be a standalone, unsupervised tool that can be efficiently run on a standard desktop computer. It has been made freely accessible and open-source at http://github.com/ccipd/MRQy for community use and feedback.

Dataset Information

RawBeans: A Simple, Vendor-Independent, Raw-Data Quality-Control Tool.

Publications

RawBeans: A Simple, Vendor-Independent, Raw-Data Quality-Control Tool.

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