Abstract:
:In this Letter, we reanalyze published mass spectrometry data sets of clinical samples with a focus on determining the coinfection status of individuals infected with SARS-CoV-2 coronavirus. We demonstrate the use of ComPIL 2.0 software along with a metaproteomics workflow within the Galaxy platform to detect cohabitating potential pathogens in COVID-19 patients using mass spectrometry-based analysis. From a sample collected from gargling solutions, we detected Streptococcus pneumoniae (opportunistic and multidrug-resistant pathogen) and Lactobacillus rhamnosus (a probiotic component) along with SARS-Cov-2. We could also detect Pseudomonas sps. Bc-h from COVID-19 positive samples and Acinetobacter ursingii and Pseudomonas monteilii from COVID-19 negative samples collected from oro- and nasopharyngeal samples. We believe that the early detection and characterization of coinfections by using metaproteomics from COVID-19 patients will potentially impact the diagnosis and treatment of patients affected by SARS-CoV-2 infection.
journal_name
J Proteome Resjournal_title
Journal of proteome researchauthors
Thuy-Boun PS,Mehta S,Gruening B,McGowan T,Nguyen A,Rajczewski AT,Johnson JE,Griffin TJ,Wolan DW,Jagtap PDdoi
10.1021/acs.jproteome.0c00822subject
Has Abstractpub_date
2021-01-04 00:00:00eissn
1535-3893issn
1535-3907pub_type
杂志文章abstract::A proteoform family is a group of related molecular forms of a protein (proteoforms) derived from the same gene. We have previously described a strategy to identify proteoforms and elucidate proteoform families in complex mixtures of intact proteins. The strategy is based upon measurements of two properties for each p...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/acs.jproteome.7b00516
更新日期:2017-11-03 00:00:00
abstract::Broadly neutralizing antibodies (bNAbs) that target the trimeric HIV-1 envelope glycoprotein spike (Env) are tools that can guide the design of recombinant Env proteins intended to engage the predicted human germline precursors of bNAbs (gl-bNAbs). The protein components of gl-bNAb epitopes are often masked by glycans...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/acs.jproteome.7b00639
更新日期:2018-03-02 00:00:00
abstract::The present study reports an in-depth proteome analysis of two Lactobacillus rhamnosus strains, the well-known probiotic strain GG and the dairy strain Lc705. We used GeLC-MS/MS, in which proteins are separated using 1-DE and identified using nanoLC-MS/MS, to generate high-quality protein catalogs. To maximize the num...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr2000896
更新日期:2011-08-05 00:00:00
abstract::Protein phosphorylation is essential for numerous cellular processes. Large-scale profiling of phosphoproteins continues to enhance the depth and speed at which we understand these processes. The development of effective phosphoprotein and peptide enrichment techniques and improvements to mass spectrometric instrument...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr060559j
更新日期:2007-03-01 00:00:00
abstract::The production of virus-like particles (VLPs) has gained importance over the last few years owing to the benefits they provide compared to conventional vaccines. The biopharmaceutical industry is currently searching for safer candidates based on VLPs for new and existing vaccines and implementing new methods of manufa...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/acs.jproteome.9b00601
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abstract::Diabetes mellitus is a complex polygenic disease caused by gene-environment interactions with multiple complications, and metabonomic analysis is crucial for pathogenesis, early diagnosis, and timely interventions. Here, we comprehensively analyzed the dynamic metabolic changes in rat urine and plasma, which were indu...
journal_title:Journal of proteome research
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更新日期:2012-06-01 00:00:00
abstract::Although some outer membrane (OM) proteins involved in antibiotic resistance have been previously reported, the OM proteins regulating chlortetracycline (CTC) resistance are largely unknown. In this study, we employed a subproteomics approach to identify altered OM proteins of Escherichia coli in response to CTC expos...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr100740w
更新日期:2010-11-05 00:00:00
abstract::Automated sequencing of unknowns in bottom-up proteomics makes the data produced susceptible to process control errors, which can be propagated into mistakes in analyte identification. Inclusion of an unintrusive internal standard, such as lysozyme, allows monitoring all phases of the proteomics process including samp...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr049819s
更新日期:2005-01-01 00:00:00
abstract::Neutrophilic granulocytes play a major role in the initiation and resolution of the inflammatory response, and demonstrate significant transcriptional and translational activity. Although much was known about neutrophils prior to the introduction of proteomics, the use of MS-based methodologies has provided an unprece...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr1000253
更新日期:2010-04-05 00:00:00
abstract::Affinity purification coupled to 1-D gel-free liquid chromatography mass spectrometry (LC-MS) is a well-established and widespread approach for the analyses of noncovalently interacting protein complexes. In this study, two proteins conjugated to a streptavidin-binding peptide and hemagglutinin double tag were express...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr4009892
更新日期:2014-02-07 00:00:00
abstract::During the development of cancer, changes in cellular glycosylation are observed, indicating that alterations of the glycome occur in extracellular fluids as well as in serum and could therefore serve as tumor biomarkers. In the case of epithelial ovarian cancer (EOC), common tumor markers such as CA125 are known to h...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr400405x
更新日期:2013-09-06 00:00:00
abstract::Proteomics by mass spectrometry (MS) allows the large-scale identification and quantitation of the cellular proteins in a given biological context. Systems biology studies from proteomics data are largely limited by the accuracy and coverage of quantitative proteomics along with missing values. Toward this end, statis...
journal_title:Journal of proteome research
pub_type: 杂志文章,评审
doi:10.1021/acs.jproteome.9b00228
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abstract::Huntington's disease (HD) is a neurodegenerative disorder caused by expansion of a CAG repeat within the Huntingtin (HTT) gene, though the clinical presentation of disease and age-of-onset are strongly influenced by ill-defined environmental factors. We recently reported a gene-environment interaction wherein expressi...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr200839d
更新日期:2012-02-03 00:00:00
abstract::Plasma biomarkers of exposure to environmental contaminants play an important role in early detection of disease. The emerging field of proteomics presents an attractive opportunity for candidate biomarker discovery, as it simultaneously measures and analyzes a large number of proteins. This article presents a case st...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr070491n
更新日期:2008-01-01 00:00:00
abstract::Proteogenomic searching is a useful method for identifying novel proteins, annotating genes and detecting peptides unique to an individual genome. The approach, however, can be laborious, as it often requires search segmentation and the use of several unintegrated tools. Furthermore, many proteogenomic efforts have be...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr400208w
更新日期:2013-06-07 00:00:00
abstract::Human embryonic stem cells (hESCs) are promising in regenerative medicine (RM) due to their differentiation plasticity and proliferation potential. However, a major challenge in RM is the generation of a vascular system to support nutrient flow to newly synthesized tissues. Here we refined an existing method to genera...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/acs.jproteome.6b00180
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abstract::Acute stress may trigger systemic biochemical and physiological changes in living organisms, leading to a rapid loss of homeostasis, which can be gradually reinstated by self-regulatory mechanisms and/or drug intervention strategy. However, such a sophisticated metabolic regulatory process has so far been poorly under...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr070051w
更新日期:2007-09-01 00:00:00
abstract::Target-decoy approach (TDA) is the dominant strategy for false discovery rate (FDR) estimation in mass-spectrometry-based proteomics. One of its main applications is direct FDR estimation based on counting of decoy matches above a certain score threshold. The corresponding equations are widely employed for filtering o...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/acs.jproteome.6b00144
更新日期:2017-02-03 00:00:00
abstract::Urine is an ideal material to study the cancer-related protein biomarkers in bladder, whereas exploration to these candidates is confronting technique challenges. Herein, we propose a comprehensive strategy of searching the urine proteins related with bladder cancer. The strategy consists of three core combinations, s...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/acs.jproteome.6b00106
更新日期:2016-07-01 00:00:00
abstract::Dendritic cells (DCs), the most potent and specialized antigen-presenting cells, play a key role in the regulation of the adaptive immunity. Immature DCs were generated by in vitro culturing of peripheral blood monocytes and functionally activated with the classical pathogen-associated molecular pattern lipopolysaccha...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr8011039
更新日期:2009-06-01 00:00:00
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journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr060406w
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abstract::A glycomic approach is developed to identify oligosaccharide markers for ovarian cancer by rapidly profiling globally released oligosaccharides. Glycoproteins shed by cancer cells are found in the supernatant (or conditioned media) of cultured cells. In this approach, shed glycoproteins are profiled for their oligosac...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr060010k
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journal_title:Journal of proteome research
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doi:10.1021/pr500688g
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journal_title:Journal of proteome research
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doi:10.1021/acs.jproteome.5b00039
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journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/acs.jproteome.0c00036
更新日期:2020-06-05 00:00:00
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journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/acs.jproteome.5b00299
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abstract::Today's highly accurate spectra provided by modern tandem mass spectrometers offer considerable advantages for the analysis of proteomic samples of increased complexity. Among other factors, the quantity of reliably identified peptides is considerably influenced by the peptide identification algorithm. While most wide...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr500202e
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journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr200872s
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journal_title:Journal of proteome research
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journal_title:Journal of proteome research
pub_type: 杂志文章
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