scholarly journals Implementing the re-use of public DIA proteomics datasets: from the PRIDE database to Expression Atlas

2021 ◽  
Author(s):  
Mathias Walzer ◽  
David Garcia-Seisdedos ◽  
Ananth Prakash ◽  
Paul Brack ◽  
Peter Crowther ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Statistical Analysis ◽  
Free Software ◽  
Analysis Software ◽  
Analysis Pipeline ◽  
The Public ◽  
Data Independent Acquisition ◽  
Metadata Annotation ◽  
Expression Atlas ◽  
Quantitative Results

Rising numbers of mass spectrometry proteomics datasets available in the public domain, increasingly include volumes generated from Data Independent Acquisition approaches, SWATH-MS in particular. Unlike Data Dependent Acquisition datasets, their re-use is limited, partially due to challenges in combination and use of free software for analysis in the non-specialist laboratory. We introduce a (re-)analysis pipeline for SWATH-MS data available in the PRIDE database, which includes a harmonised combination of metadata annotation protocols, automated workflows for MS data, statistical analysis and results integration into the resource Expression Atlas. Automation is orchestrated with Nextflow, using containerised open analysis software tools, rendering the pipeline readily available, reproducible and easy to update. To demonstrate its utility, we reanalysed 10 public DIA datasets, 1,278 individual SWATH-MS runs, stored in PRIDE. The robustness of the analysis was evaluated and compared to the results obtained in the original publications. The final results were exported into Expression Atlas, making quantitative results from SWATH-MS experiments more widely available and integrated with results from other reanalysed proteomics and transcriptomics datasets.

scholarly journals Arabidopsis Proteome and the Mass Spectral Assay Library

2019 ◽  
Author(s):  
Huoming Zhang ◽  
Pei Liu ◽  
Tiannan Guo ◽  
Huayan Zhao ◽  
Dalila Bensaddek ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Abscisic Acid ◽  
Acid Stress ◽  
Model Organism ◽  
Mass Spectrometry Data ◽  
Mass Spectral ◽  
Novel Proteins ◽  
Data Independent Acquisition ◽  
Arabidopsis Proteome ◽  
Expression Atlas

AbstractArabidopsis is an important model organism and the first plant with its genome sequenced. Knowledge from studying this species has either direct or indirect applications to agriculture and human health. Quantitative proteomics by data-independent acquisition (SWATH/DIA-MS) was recently developed and considered as a high-throughput targetedlike approach for accurate proteome quantitation. In this approach, a high-quality and comprehensive library is a prerequisite. Here, we generated a protein expression atlas of 10 organs of Arabidopsis and created a library consisting of 15,514 protein groups, 187,265 unique peptide sequences, and 278,278 precursors. The identified protein groups correspond to ~56.5% of the predicted proteome. Further proteogenomics analysis identified 28 novel proteins. We subsequently applied DIA-mass spectrometry using this library to quantify the effect of abscisic acid on Arabidopsis. We were able to recover 8,793 protein groups with 1,787 of them being differentially expressed which includes 65 proteins known to respond to abscisic acid stress. Mass spectrometry data are available via ProteomeXchange with identifier PXD012710 for data-dependent acquisition and PXD014032 for DIA analyses.

scholarly journals mapDIA: Preprocessing and statistical analysis of quantitative proteomics data from data independent acquisition mass spectrometry

2015 ◽  
Vol 129 ◽  
pp. 108-120 ◽  
Author(s):  
Guoshou Teo ◽  
Sinae Kim ◽  
Chih-Chiang Tsou ◽  
Ben Collins ◽  
Anne-Claude Gingras ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Statistical Analysis ◽  
Quantitative Proteomics ◽  
Proteomics Data ◽  
Data Independent Acquisition

scholarly journals Sisvar: a computer statistical analysis system

2011 ◽  
Vol 35 (6) ◽  
pp. 1039-1042 ◽  
Author(s):  
Daniel Furtado Ferreira
Keyword(s):  
Statistical Analysis ◽  
Programming Language ◽  
Scientific Community ◽  
Free Software ◽  
Exact Science ◽  
Analysis Software ◽  
The Third ◽  
Statistical Analysis System ◽  
Analysis System ◽  
Statistical Analysis Software

Sisvar is a statistical analysis system, first released in 1996 although its development began in 1994. The first version was done in the programming language Pascal and compiled with Borland Turbo Pascal 3. Sisvar was developed to achieve some specific goals. The first objective was to obtain software that could be used directly on the statistical experimental course of the Department of Exact Science at the Federal University of Lavras. The second objective was to initiate the development of a genuinely Brazilian free software program that met the demands and peculiarities of research conducted in the country. The third goal was to present statistical analysis software for the Brazilian scientific community that would allow research results to be analyzed efficiently and reliably. All of the initial goals were achieved. Sisvar gained acceptance by the scientific community because it provides reliable, accurate, precise, simple and robust results, and allows users a greater degree of interactivity.

scholarly journals Quantitative Analysis of Pyrazines and Their Perceptual Interactions in Soy Sauce Aroma Type Baijiu

Foods ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 441
Author(s):  
Yan Yan ◽  
Shuang Chen ◽  
Yao Nie ◽  
Yan Xu
Keyword(s):  
Mass Spectrometry ◽  
Quantitative Analysis ◽  
Ultra Performance Liquid Chromatography ◽  
Alcohol Solution ◽  
Soy Sauce ◽  
Tandem Mass ◽  
Odor Thresholds ◽  
Quantitative Results ◽  
Odor Activity Value ◽  
The Impact

Pyrazines are important compounds in soy sauce aroma type Baijiu (SSAB). In this work, a total of 16 pyrazines were analyzed using ultra-performance liquid chromatography coupled with tandem mass spectrometry (UPLC–MS/MS) in SSAB. The quantitative results showed that 2,3,5,6-tetramethylpyrazine, 2,6-dimethylpyrazine and 2,3,5-trimethylpyrazine were the three most concentrated pyrazines. The highest odor activity value (OAV) was determined for 2-ethyl-3,5-dimethylpyrazine. Quantitative analysis combined with descriptive sensory analysis revealed that sub-threshold pyrazines (2,3-dimethylpyrazine, 2,3-diethylpyrazine, 2,3-diethyl-5-methylpyrazine and 2-acetyl-3-methylpyrazine) are significantly correlated with the roasted aroma in SSAB. Our study focused on the impact of sub-threshold pyrazines on the perception of roasted aroma in SSAB. The effect of the sub-threshold pyrazines was detected by the addition of various pyrazines in SSAB samples, despite their sub-threshold concentrations. Furthermore, the presence of sub-threshold pyrazines in dilute alcohol solution resulted in a significant reduction in the odor thresholds of supra-threshold pyrazines. Sensory investigation indicated that pyrazines have a synergistic effect on the perception of roasted aroma. The results highlighted the contribution of some pyrazines to the roasted aroma in SSAB despite their sub-threshold concentrations.

scholarly journals Affective communication: a mixed method investigation into COVID-19 outbreak communication using the Taiwanese government Facebook page

2021 ◽  
pp. 175797592110035
Author(s):  
Chia Yu Lien ◽  
Yun-Hsuan Wu
Keyword(s):  
Social Media ◽  
Mixed Method ◽  
Health Authority ◽  
Disease Outbreak ◽  
Government Agencies ◽  
Affective Communication ◽  
Frontline Workers ◽  
The Public ◽  
Qualitative And Quantitative ◽  
Quantitative Results

The COVID-19 outbreak has created an unprecedented challenge for governments to convey information to the public, and social media has become a critical method of COVID-19 communication in Taiwan. Objectives: This study examines a total of 1128 Facebook posts published by Taiwan’s principal health authority from December 1, 2019 to May 31, 2020. Methods: Using both qualitative and quantitative approaches, this study investigates strategies used by the Taiwan government to communicate the COVID-19 outbreak and public responses toward these strategies. Result: Novel uses of Facebook posts on outbreak communication were identified, including solidarity, reviews of actions, press conferences, and the use of animal and cartoon images. Quantitative results showed that the public responded significantly more frequently to messages generating positive affects, such as posts that reviewed government actions and public efforts; posts that expressed thanks, approval, or comradeship; and posts that paired text with photographs of frontline workers or cute animals. Conclusion: These results suggest that, amid a disease outbreak, the public not only look for updated situations and guidelines but also for affective affirmation from government agencies.

scholarly journals A quantitative analysis software tool for mass spectrometry–based proteomics

2008 ◽  
Vol 5 (4) ◽  
pp. 319-322 ◽  
Author(s):  
Sung Kyu Park ◽  
John D Venable ◽  
Tao Xu ◽  
John R Yates
Keyword(s):  
Mass Spectrometry ◽  
Quantitative Analysis ◽  
Software Tool ◽  
Analysis Software
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