scholarly journals Recent advances in software tools for more generic and precise intact glycopeptide analysis

2020 ◽  
pp. mcp.R120.002090 ◽  
Author(s):  
Weiqian Cao ◽  
Mingqi Liu ◽  
Siyuan Kong ◽  
Mengxi Wu ◽  
Yang Zhang ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Systematic Review ◽  
Quality Control ◽  
Software Tools ◽  
Mass Spectrometry Data ◽  
Identification Process ◽  
Advantages And Disadvantages ◽  
Recent Advances ◽  
Glycopeptide Analysis

Intact glycopeptide identification has long been known as a key and challenging barrier to the comprehensive and accurate understanding the role of glycosylation in an organism. Intact glycopeptide analysis is a blossoming field that has received increasing attention in recent years. Mass spectrometry (MS)-based strategies and relative software tools are major drivers that have greatly facilitated the analysis of intact glycopeptides, particularly intact N-glycopeptides. This manuscript provides a systematic review of the intact glycopeptide identification process using mass spectrometry data generated in shotgun proteomic experiments, which typically focus on N-glycopeptide analysis. Particular attention is paid to the software tools that have been recently developed in the last decade for the interpretation and quality control of glycopeptide spectra acquired using different MS strategies. The review also provides information about the characteristics and applications of these software tools, discusses their advantages and disadvantages, and concludes with a discussion of outstanding tools.

Recent advances in mass-spectrometry based proteomics software, tools and databases

2021 ◽  
Author(s):  
Ankit Halder ◽  
Ayushi Verma ◽  
Deeptarup Biswas ◽  
Sanjeeva Srivastava
Keyword(s):  
Mass Spectrometry ◽  
Software Tools ◽  
Recent Advances

scholarly journals Breastfeeding and COVID-19: From Nutrition to Immunity

2021 ◽  
Vol 12 ◽  
Author(s):  
Emilia Vassilopoulou ◽  
Gavriela Feketea ◽  
Lemonica Koumbi ◽  
Christina Mesiari ◽  
Elena Camelia Berghea ◽  
...  
Keyword(s):  
Systematic Review ◽  
Breast Milk ◽  
Respiratory Viruses ◽  
Advantages And Disadvantages ◽  
Body Of Knowledge ◽  
Mother And Child ◽  
Neonatal Immune System ◽  
Protection Against Infection ◽  
Available Information

Breastfeeding not only provides the optimum source of nutrients for the neonate and its first strong shield against infection but also lays the foundation for somatic and psychological bonding between the mother and child. During the current COVID-19 pandemic, although the guidelines of the relevant international and national agencies recommend breastfeeding by SARS-CoV-2–infected mothers, considerable insecurity persists in daily clinical practice regarding the safety of the infants and the perceived advantages and disadvantages of discontinuation of breastfeeding. This is a systematic review of the currently available information regarding the transmissibility of SARS-CoV-2 through or while breastfeeding and the protection against infection that breast milk might provide. The accumulated body of knowledge regarding the role of breast milk in the development of the neonatal immune system and protection against infection by other respiratory viruses is discussed, with a focus on the anti-inflammatory role of the antibodies, microbes, and viruses provided to the infant in breast milk and its relevance to the case of SARS-CoV-2.

scholarly journals Systematic Identification of Protein Phosphorylation-Mediated Interactions

2020 ◽  
Author(s):  
Brendan M. Floyd ◽  
Kevin Drew ◽  
Edward M. Marcotte
Keyword(s):  
Mass Spectrometry ◽  
Protein Phosphorylation ◽  
Protein Interactions ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Specific Protein ◽  
Mass Spectrometry Data ◽  
Size Exclusion ◽  
Functional Protein

ABSTRACTProtein phosphorylation is a key regulatory mechanism involved in nearly every eukaryotic cellular process. Increasingly sensitive mass spectrometry approaches have identified hundreds of thousands of phosphorylation sites but the functions of a vast majority of these sites remain unknown, with fewer than 5% of sites currently assigned a function. To increase our understanding of functional protein phosphorylation we developed an approach for identifying the phosphorylation-dependence of protein assemblies in a systematic manner. A combination of non-specific protein phosphatase treatment, size-exclusion chromatography, and mass spectrometry allowed us to identify changes in protein interactions after the removal of phosphate modifications. With this approach we were able to identify 316 proteins involved in phosphorylation-sensitive interactions. We recovered known phosphorylation-dependent interactors such as the FACT complex and spliceosome, as well as identified novel interactions such as the tripeptidyl peptidase TPP2 and the supraspliceosome component ZRANB2. More generally, we find phosphorylation-dependent interactors to be strongly enriched for RNA-binding proteins, providing new insight into the role of phosphorylation in RNA binding. By searching directly for phosphorylated amino acid residues in mass spectrometry data, we identified the likely regulatory phosphosites on ZRANB2 and FACT complex subunit SSRP1. This study provides both a method and resource for obtaining a better understanding of the role of phosphorylation in native macromolecular assemblies.

scholarly journals MALDIrppa: quality control and robust analysis for mass spectrometry data

2017 ◽  
Vol 34 (3) ◽  
pp. 522-523 ◽  
Author(s):  
Javier Palarea-Albaladejo ◽  
Kevin Mclean ◽  
Frank Wright ◽  
David G E Smith
Keyword(s):  
Mass Spectrometry ◽  
Quality Control ◽  
Mass Spectrometry Data ◽  
Robust Analysis

scholarly journals ROLE OF WHATSAPP® IN MEDICAL EDUCATION: A LITERATURE REVIEW

2019 ◽  
Vol 2 (2) ◽  
pp. 60-65
Author(s):  
Noor-i-Kiran Naeem ◽  
Rehan Ahmed Khan ◽  
Haris Iqbal
Keyword(s):  
Systematic Review ◽  
Medical Education ◽  
Medical Students ◽  
Conclusive Evidence ◽  
Educational Effectiveness ◽  
Inclusion Criteria ◽  
Advantages And Disadvantages ◽  
Research Type ◽  
Share Information

ABSTRACT Background: This review is aimed to find out how WhatsApp® has been integrated into medical education. A systematic review of the current literature was performed, links to prior reviews were drawn and implications for the future were discussed. Methods: Three databases (PubMed, ERIC and Science Direct) were searched after defining the inclusion criteria. Key information from the articles was methodically abstracted and discussed in the categories research type, study design, participants' level of medical education and study content along with the use of WhatsApp® in Medical education and its perceived advantages and disadvantages. Results: Fourteen articles met the inclusion criteria. Results showed that 40-76% of medical students had a WhatsApp® account out of which 30- 60% used WhatsApp® for educational purposes. WhatsApp® was used to communicate with fellow students and faculty, share information online and participate in discussions groups. Conclusion: WhatsApp® influences a myriad of aspects of medical education at the undergraduate and graduate level. Despite an increase in the use of WhatsApp® in medical education, there is a lack of conclusive evidence in terms of its educational effectiveness.

Evaluation of Trans-laminar Facet Screw for Lumbar Spine Fixation and Fusion: A Systematic Review

QJM ◽  
2021 ◽  
Vol 114 (Supplement_1) ◽  
Author(s):  
Omar Y Hammad ◽  
Salah M Hamada ◽  
Ibrahim A Ismaiel ◽  
Walid B El-Etr
Keyword(s):  
Systematic Review ◽  
Small Volume ◽  
Operative Time ◽  
Screw Fixation ◽  
Low Cost ◽  
Advantages And Disadvantages ◽  
Transpedicular Screw ◽  
Specialized Equipment ◽  
Spine Fixation

Abstract Background Translaminar facet screws are an excellent solution for stabilization of the vertebral motion. It is simple, does not require any specialized equipment, and has the advantages of being a procedure of lesser magnitude, lesser operative time and few complication rate. Recently there is growing interest in this technique to augment the anterior lumbar fusions to achieve global fusion less invasively. Aim of the Work to evaluate the role of translaminar facet screw in lumber fixation and fusion inclusion different techniques of translaminar facet screw fixation, its advantages and disadvantages. Methodology: This systematic review included a discussion of all available studies meeting the eligible criteria including: well conducted descriptive studies, cohort, articles, accepted manuscripts, clinical trials, analytic studies and the literature of reviews, technical notes. Results The small volume of the metal in comparison with pedicle screw constructs provides faster patient recovery and reduce the rate of infection and also provide an adequate area for placement of bone grafts. The low cost of the implants is an added advantage in view of the rising costs of health care. Conclusion Translaminar facet screw fixation is feasible, cheaper and effective in lumbar fixation. The technique is not demanding as transpedicular screw with easier learning curve.

scholarly journals Quality Control and Outlier Detection of Targeted Mass Spectrometry Data from Multiplex Protein Panels

2020 ◽  
Vol 19 (6) ◽  
pp. 2278-2293
Author(s):  
Irene van den Broek ◽  
Mitra Mastali ◽  
Kelly Mouapi ◽  
Cory Bystrom ◽  
C. Noel Bairey Merz ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Quality Control ◽  
Outlier Detection ◽  
Mass Spectrometry Data
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