scholarly journals Prior Signal Acquisition Software Versions for Orbitrap Underestimate Low Isobaric Mass Tag Intensities, Without Detriment to Differential Abundance Experiments

2021 ◽  
Author(s):  
Tom S. Smith ◽  
Anja Andrejeva ◽  
Josie A. Christopher ◽  
Oliver M. Crook ◽  
Mohamed A.W. Elzek ◽  
...  
Keyword(s):  
Quantitative Proteomics ◽  
Quantitative Data ◽  
Signal Acquisition ◽  
Tandem Mass ◽  
Proteomics Data ◽  
Mixed Species ◽  
Differential Abundance ◽  
Proteomics Experiment ◽  
The Impact ◽  
Acquisition Software

Tandem mass tags (TMT) enable simple and accurate quantitative proteomics for multiplexed samples by relative quantification of tag reporter ions. Orbitrap quantification of reporter ions has been associated with a characteristic notch region in intensity distribution, within which few reporter intensities are recorded. This has been resolved in version 3 of the instrument acquisition software, Tune. However, 53 % of Orbitrap Fusion, Lumos or Eclipse submissions to PRIDE were generated using prior software versions. To quantify the impact of the notch on existing quantitative proteomics data, we generated a mixed species benchmark and acquired quantitative data using Tune versions 2 and 3. Sub-notch intensities are systemically underestimated with Tune version 2, leading to over-estimation of the true differences in intensities between samples. However, when summarising reporter ion intensities to higher level features, such as peptides and proteins, few features are significantly affected. Targeted removal of spectra with reporter ion intensities below the notch is not beneficial for differential peptide or protein testing. Overall, we find the systematic quantification bias associated with the notch is not detrimental for a typical proteomics experiment.

scholarly journals Oxonium Ion Guided Analysis of Quantitative Proteomics Data Reveals Site-Specific O-Glycosylation of Anterior Gradient Protein 2 (AGR2)

2021 ◽  
Vol 22 (10) ◽  
pp. 5369
Author(s):  
Martina Pirro ◽  
Yassene Mohammed ◽  
Arnoud H. de Ru ◽  
George M. C. Janssen ◽  
Rayman T. N. Tjokrodirijo ◽  
...  
Keyword(s):  
Cell Lines ◽  
Quantitative Proteomics ◽  
Glycosylation Site ◽  
Total Cell ◽  
Tandem Mass ◽  
Proteomics Data ◽  
Site Specific ◽  
Oxonium Ions ◽  
Tandem Mass Tag ◽  
Colorectal Cancer Cell Lines

Developments in mass spectrometry (MS)-based analyses of glycoproteins have been important to study changes in glycosylation related to disease. Recently, the characteristic pattern of oxonium ions in glycopeptide fragmentation spectra had been used to assign different sets of glycopeptides. In particular, this was helpful to discriminate between O-GalNAc and O-GlcNAc. Here, we thought to investigate how such information can be used to examine quantitative proteomics data. For this purpose, we used tandem mass tag (TMT)-labeled samples from total cell lysates and secreted proteins from three different colorectal cancer cell lines. Following automated glycopeptide assignment (Byonic) and evaluation of the presence and relative intensity of oxonium ions, we observed that, in particular, the ratio of the ions at m/z 144.066 and 138.055, respectively, could be used to discriminate between O-GlcNAcylated and O-GalNAcylated peptides, with concomitant relative quantification between the different cell lines. Among the O-GalNAcylated proteins, we also observed anterior gradient protein 2 (AGR2), a protein which glycosylation site and status was hitherto not well documented. Using a combination of multiple fragmentation methods, we then not only assigned the site of modification, but also showed different glycosylation between intracellular (ER-resident) and secreted AGR2. Overall, our study shows the potential of broad application of the use of the relative intensities of oxonium ions for the confident assignment of glycopeptides, even in complex proteomics datasets.

scholarly journals Comparison of TIMS-PASEF quantitative proteomics data-analysis workflows using FragPipe, DIA-NN, and Spectronaut from a user's perspective

2021 ◽  
Author(s):  
Alejandro Fernandez-Vega ◽  
Federica Farabegoli ◽  
Maria Mercedes Alonso-Martinez ◽  
Ignacio Ortea
Keyword(s):  
Data Analysis ◽  
Quantitative Proteomics ◽  
Real Life ◽  
Analysis Tool ◽  
Proteomics Data ◽  
Mass Spectrometers ◽  
Data Independent Acquisition ◽  
Proteomics Experiment ◽  
Under Sampling ◽  
The One

Data-independent acquisition (DIA) methods have gained great popularity in bottom-up quantitative proteomics, as they overcome the irreproducibility and under-sampling limitations of data-dependent acquisition (DDA). diaPASEF, recently developed for the timsTOF Pro mass spectrometers, has brought improvements to DIA, providing additional ion separation (in the ion mobility dimension) and increasing sensitivity. Several studies have benchmarked different workflows for DIA quantitative proteomics, but mostly using instruments from Sciex and Thermo, and therefore, the results are not extrapolable to diaPASEF data. In this work, using a real-life sample set like the one that can be found in any proteomics experiment, we compared the results of analyzing PASEF data with different combinations of library-based and library-free analysis, combining the tools of the FragPipe suite, DIA-NN and including MS1-level LFQ with DDA-PASEF data, and also comparing with the workflows possible in Spectronaut. We verified that library-independent workflows, not so efficient not so long ago, have greatly improved in the recent versions of the software tools, and now perform as well or even better than library-based ones. We report here information so that the user who is going to conduct a relative quantitative proteomics study using a timsTOF Pro mass spectrometer can make an informed decision on how to acquire (diaPASEF for DIA analysis, or DDA-PASEF for MS1-level LFQ) the samples, and what can be expected depending on the data analysis tool used, among the different alternatives offered by the recently optimized tools for TIMS-PASEF data analysis.

scholarly journals Multi-omics Analyses Reveal Synergistic Carbohydrate Metabolism in Streptococcus mutans-Candida albicans Mixed-Species Biofilms

2019 ◽  
Vol 87 (10) ◽  
Author(s):  
K. Ellepola ◽  
T. Truong ◽  
Y. Liu ◽  
Q. Lin ◽  
T. K. Lim ◽  
...  
Keyword(s):  
Candida Albicans ◽  
Carbohydrate Metabolism ◽  
Streptococcus Mutans ◽  
Quantitative Proteomics ◽  
Sugar Transport ◽  
Oral Disease ◽  
Mixed Species ◽  
Carbohydrate Utilization ◽  
Content Type ◽  
The Impact

ABSTRACT Candida albicans, a major opportunistic fungal pathogen, is frequently found together with Streptococcus mutans in dental biofilms associated with severe childhood caries (tooth decay), a prevalent pediatric oral disease. However, the impact of this cross-kingdom relationship on C. albicans remains largely uncharacterized. Here, we employed a novel quantitative proteomics approach in conjunction with transcriptomic profiling to unravel molecular pathways of C. albicans when cocultured with S. mutans in mixed biofilms. RNA sequencing and iTRAQ (isobaric tags for relative and absolute quantitation)-based quantitative proteomics revealed that C. albicans genes and proteins associated with carbohydrate metabolism were significantly enhanced, including sugar transport, aerobic respiration, pyruvate breakdown, and the glyoxylate cycle. Other C. albicans genes and proteins directly and indirectly related to cell morphogenesis and cell wall components such as mannan and glucan were also upregulated, indicating enhanced fungal activity in mixed-species biofilm. Further analyses revealed that S. mutans-derived exoenzyme glucosyltransferase B (GtfB), which binds to the fungal cell surface to promote coadhesion, can break down sucrose into glucose and fructose that can be readily metabolized by C. albicans, enhancing growth and acid production. Altogether, we identified key pathways used by C. albicans in the mixed biofilm, indicating an active fungal role in the sugar metabolism and environmental acidification (key virulence traits associated with caries onset) when interacting with S. mutans, and a new cross-feeding mechanism mediated by GtfB that enhances C. albicans carbohydrate utilization. In addition, we demonstrate that comprehensive transcriptomics and quantitative proteomics can be powerful tools to study microbial contributions which remain underexplored in cross-kingdom biofilms.

Identification of novel autoantibodies in ascites of relapsed paclitaxel-resistant gastric cancer with peritoneal metastasis using immunome protein microarrays and proteomics

2021 ◽  
pp. 1-10
Author(s):  
Zhongyin Yang ◽  
Chao Yan ◽  
Wentao Liu ◽  
Wei Xu ◽  
Chen Li ◽  
...  
Keyword(s):  
Gastric Cancer ◽  
Effective Treatment ◽  
Peritoneal Metastasis ◽  
Quantitative Proteomics ◽  
Poor Prognosis ◽  
Protein Microarrays ◽  
Tandem Mass ◽  
Tandem Mass Tag ◽  
Resistant Group ◽  
Potential Biomarkers

BACKGROUND: Gastric cancer (GC) patients with peritoneal metastasis usually have extremely poor prognosis. Intraperitoneal infusion of paclitaxel (PTX) provides an effective treatment, but relapse and PTX-resistance are unavoidable disadvantages, and it is difficult to monitor the occurrence of PTX-resistance. OBJECTIVE: The aim of this study was to explore novel autoantibodies in the ascites of individuals with relapsed PTX-resistant GC with peritoneal metastasis. METHODS: Ascites samples were collected before PTX infusion and after the relapse in 3 GC patients. To determine the expression of significantly changed proteins, we performed autoantibody profiling with immunome protein microarrays and tandem mass tag (TMT) quantitative proteomics, and then, the overlapping proteins were selected. RESULTS: Thirty-eight autoantibodies that were differentially expressed between the ascites in the untreated group and relapsed PTX-resistant group were identified. For confirmation of the results, TMT quantitative proteomics was performed, and 842 dysregulated proteins were identified. Four proteins, TPM3, EFHD2, KRT19 and vimentin, overlapped between these two assays. CONCLUSIONS: Our results first revealed that TPM3, EFHD2, KRT19 and vimentin were novel autoantibodies in the ascites of relapsed PTX-resistant GC patients. These autoantibodies may be used as potential biomarkers to monitor the occurrence of PTX-resistance.

scholarly journals Evaluation of the effect of the capitation compensation mechanism among pulmonary tuberculosis patients with a full period of treatment

2021 ◽  
Vol 10 (1) ◽  
Author(s):  
Xing-Yu Hu ◽  
Guang-Ying Gao
Keyword(s):  
Pulmonary Tuberculosis ◽  
Patient Compliance ◽  
Quantitative Data ◽  
Financial Burden ◽  
Descriptive Analysis ◽  
Compensation Mechanism ◽  
Medication Costs ◽  
Implementation Time ◽  
Full Period ◽  
The Impact

Abstract Background PTB is an infectious disease, which not only seriously affects people’s health, but also causes a heavier disease economic burden on patients. At present, reform of the medical insurance payment can be an effective method to control medical expenses. Therefore, our study is to explore the compensation mechanism for pulmonary tuberculosis (PTB) patients with a full period of treatment, to alleviate the financial burden of PTB patients and provide a reference and basis for the reform of PTB payment methods in other regions and countries. Methods The quantitative data of PTB patients was collected from the first half of 2015 to the first half of 2018 in Dehui Tuberculosis Hospital in Jilin Province, and medical records of PTB patients registered in the first half of 2018 (n = 100) from the hospital was randomly selected. Descriptive analysis of these quantitative data summarized the number, cost, medication and compliance. Semi-structured in depth interviews with policymakers and physicians were conducted to understand the impact of interventions and its causes. Results After implementation of the compensation mechanism, the number of PTB patient visits in 2018 was increased by 14.2%, average medical costs for outpatients and inpatients were significantly reduced by 31.8% and 47.0%, respectively, and the auxiliary medication costs was reduced by 36.5%. Moreover, the hospital carried out standardized management of tuberculosis, and the patient compliance was very high, reaching almost 90%. Conclusions The capitation compensation mechanism with a full period of treatment was a suitable payment method for PTB, and it is worthy of promotion and experimentation. In addition, the model improved patient compliance and reduced the possibility of drug-resistant PTB. However, due to the short implementation time of the model in the pilot areas, the effect remains to be further observed and demonstrated.

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 Analyzing Factors Affecting the Sustainability of Land Management Practices in Mecha Woreda, Northwestern Ethiopia

2021 ◽  
Vol 13 (13) ◽  
pp. 7007
Author(s):  
Habtamu Nebere ◽  
Degefa Tolossa ◽  
Amare Bantider
Keyword(s):  
Decision Making ◽  
Land Management ◽  
Land Degradation ◽  
Quantitative Data ◽  
Management Practices ◽  
Short Term ◽  
Factors Affecting ◽  
Decision Making Processes ◽  
Household Heads ◽  
The Impact

In Ethiopia, the practice of land management started three decades ago in order to address the problem of land degradation and to further boost agricultural production. However, the impact of land management practices in curbing land degradation problems and improving the productivity of the agricultural sector is insignificant. Various empirical works have previously identified the determinants of the adoption rate of land management practices. However, the sustainability of land management practices after adoption, and the various factors that control the sustainability of implemented land management practices, are not well addressed. This study analyzed the factors affecting the sustainability of land management practices after implementation in Mecha Woreda, northwestern Ethiopia. The study used 378 sample respondents, selected by a systematic random sampling technique. Binary logistic regression was used to analyze the quantitative data, while the qualitative data were qualitatively and concurrently analyzed with the quantitative data. The sustained supply of fodder from the implemented land management practices, as well as improved cattle breed, increases the sustainability of the implemented land management practices. While lack of agreement in the community, lack of enforcing community bylaws, open cattle grazing, lack of benefits of implemented land management practices, acting as barrier for farming practices, poor participation of household heads during planning and decision-making processes, as well as the lack of short-term benefits, reduce the sustainability of the implemented land management practices. Thus, it is better to allow for the full participation of household heads in planning and decision-making processes to bring practical and visible results in land management practices. In addition, recognizing short-term benefits to compensate the land lost in constructing land management structures must be the strategy in land management practices. Finally, reducing the number of cattle and practicing stall feeding is helpful both for the sustainability of land management practices and the productivity of cattle. In line with this, fast-growing fodder grass species have to be introduced for household heads to grow on land management structures and communal grazing fields for stall feeding.

Determination of multi pesticide residues in leaf and needle samples using a modified QuEChERS approach and gas chromatography-tandem mass spectrometry

2021 ◽  
Author(s):  
Arnelle Löbbert ◽  
Sonja Schanzer ◽  
Henrik Krehenwinkel ◽  
Franz Bracher ◽  
Christoph Müller
Keyword(s):  
Mass Spectrometry ◽  
Gas Chromatography ◽  
Tandem Mass Spectrometry ◽  
Forest Ecosystems ◽  
Tandem Mass ◽  
Modified Quechers ◽  
Chromatography Tandem Mass Spectrometry ◽  
The Impact ◽  
Impact Of Pesticides

A novel, validated QuEChERS-based GC-MS/MS method was developed, which will allow the assessment of the impact of pesticides on forest ecosystems.

scholarly journals Assessing the impact of a combined nutrition counselling and cash transfer intervention on women’s empowerment in rural Bangladesh: a randomised control trial protocol

BMJ Open ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. e044263
Author(s):  
Elizabeth K Kirkwood ◽  
Michael John Dibley ◽  
John Frederick Hoddinott ◽  
Tanvir Huda ◽  
Tracey Lea Laba ◽  
...  
Keyword(s):  
Quantitative Data ◽  
Women's Empowerment ◽  
Cash Transfer ◽  
Women’S Empowerment ◽  
Randomised Control Trial ◽  
Call Centre ◽  
Rural Bangladesh ◽  
Nutrition Counselling ◽  
The Impact ◽  
Unconditional Cash Transfer

IntroductionThere is growing interest in assessing the impact of health interventions, particularly when women are the focus of the intervention, on women’s empowerment. Globally, research has shown that interventions targeting nutrition, health and economic development can affect women’s empowerment. Evidence suggests that women’s empowerment is also an underlying determinant of nutrition outcomes. Depending on the focus of the intervention, different domains of women’s empowerment will be influenced, for example, an increase in nutritional knowledge, or greater control over income and access to resources.ObjectiveThis study evaluates the impact of the Shonjibon Cash and Counselling (SCC) Trial that combines nutrition counselling and an unconditional cash transfer, delivered on a mobile platform, on women’s empowerment in rural Bangladesh.Methods and analysisWe will use a mixed-methods approach, combining statistical analysis of quantitative data from 2840 women in a cluster randomised controlled trial examining the impact of nutrition behaviour change communications (BCCs) and cash transfers on child undernutrition. Pregnant participants will be given a smartphone with a customised app, delivering nutrition BCC messages, and will receive nutrition counselling via a call centre and an unconditional cash transfer. This study is a component of the SCC Trial and will measure women’s empowerment using a composite indicator based on the Project-Level Women’s Empowerment in Agriculture Index, with quantitative data collection at baseline and endline. Thematic analysis of qualitative data, collected through longitudinal interviews with women, husbands and mothers-in-law, will elicit a local understanding of women’s empowerment and the linkages between the intervention and women’s empowerment outcomes. This paper describes the study protocol to evaluate women’s empowerment in a nutrition-specific and sensitive intervention using internationally validated, innovative tools and will help fill the evidence gap on pathways of impact, highlighting areas to target for future programming.Ethics and disseminationEthical approval has been obtained from the International Centre for Diarrhoeal Disease Research (Ref. PR 17106) and The University of Sydney (Ref: 2019/840). Findings from this study will be shared in Bangladesh with dissemination sessions in-country and internationally at conferences, and will be published in peer-reviewed journals.

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