Abstract：
:The enormous challenges of mass spectrometry-based metaproteomics are primarily related to the analysis and interpretation of the acquired data. This includes reliable identification of mass spectra and the meaningful integration of taxonomic and functional meta-information from samples containing hundreds of unknown species. To ease these difficulties, we developed a dedicated software suite, the MetaProteomeAnalyzer, an intuitive open-source tool for metaproteomics data analysis and interpretation, which includes multiple search engines and the feature to decrease data redundancy by grouping protein hits to so-called meta-proteins. We also designed a graph database back-end for the MetaProteomeAnalyzer to allow seamless analysis of results. The functionality of the MetaProteomeAnalyzer is demonstrated using a sample of a microbial community taken from a biogas plant.
journal_name
J Proteome Resjournal_title
Journal of proteome researchauthors
Muth T,Behne A,Heyer R,Kohrs F,Benndorf D,Hoffmann M,Lehtevä M,Reichl U,Martens L,Rapp Edoi
10.1021/pr501246wsubject
Has Abstractpub_date
2015-03-06 00:00:00pages
1557-65issue
3eissn
1535-3893issn
1535-3907journal_volume
14pub_type
杂志文章abstract：:We demonstrate an approach for global quantitative analysis of protein mixtures using differential stable isotopic labeling of the enzyme-digested peptides combined with microbore liquid chromatography (LC) matrix-assisted laser desorption ionization (MALDI) mass spectrometry (MS). Microbore LC provides higher sample ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr049784w
更新日期：2005-05-01 00:00:00
abstract：:We previously described a microLC-ESI-Q-TOF MS method for identifying monoclonal immunoglobulins in serum and then tracking them over time using their accurate molecular mass. Here we demonstrate how the same methodology can be used to identify and characterize polyclonal immunoglobulins in serum. We establish that tw...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr5005967
更新日期：2014-11-07 00:00:00
abstract：:Tryptic digestion of biotinylated Lys-C peptides followed by affinity chromatography allows the selective isolation of lysine-free tryptic peptides delimited by arginine residues (RRnK peptides). In silico analysis revealed that RRnK peptides represent 87% of the whole proteomes and their specific isolation simplifies...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr060003w
更新日期：2006-05-01 00:00:00
abstract：:We have explored the potential of commercial polystyrene-divinylbenzene monolithic capillary nanoLC-MS/MS for identifying Sinorhizobium fredii HH103 nodulation outer proteins. Monolithic nanoLC with off-line MALDI-TOF/TOF and on-line ESI-q-oTOF is fast and robust, generating complementary data and offering high-confid...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr060519f
更新日期：2007-03-01 00:00:00
abstract：:Protein phosphorylation is a globally adopted and tightly controlled post-translational modification, and represents one of the most important molecular switching mechanisms that govern the entire spectrum of biological processes. In the central nervous system, it has been demonstrated that phosphorylation of key prot...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr8003198
更新日期：2008-11-01 00:00:00
abstract：:An important mechanism by which plants defend themselves against pathogens is the rapid execution of a hypersensitive response (HR). Tomato plants containing the Cf-4 resistance gene mount an HR that relies on the activation of phosphorylation cascades, when challenged with the Avr4 elicitor secreted by the pathogenic...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr800619h
更新日期：2009-03-01 00:00:00
abstract：:Yeast two-hybridization (Y2H) is a classical method to study protein-protein interactions in organisms, and the top limitation of Y2H is the high ratio of false negatives and false positives. The most efficient way to reduce this error is to improve the quality of the library. The traditional library quality evaluatio...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.0c00189
更新日期：2020-08-07 00:00:00
abstract：:Natural disasters such as drought, extreme temperatures, and flooding can severely impact crop production. Understanding the metabolic response of crops threatened with these disasters provides insights into biological response mechanisms that can influence survival. In this study, a comparative analysis of GC-MS and ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr300953k
更新日期：2013-02-01 00:00:00
abstract：:Large-scale identification of protein-protein interactions (PPIs) in functional complexes represents an efficient route to elucidate the regulatory rules of cellular functions. Whereas many methods have been developed to identify the PPIs associated with particular target/bait protein in complexes, little information ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr800662x
更新日期：2009-05-01 00:00:00
abstract：:Protein biomarkers are critical for diagnosis, prognosis, and treatment of disease. The transition from protein biomarker discovery to verification can be a rate limiting step in clinical development of new diagnostics. Liquid chromatography-selected reaction monitoring mass spectrometry (LC-SRM MS) is becoming an imp...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr2006704
更新日期：2012-02-03 00:00:00
abstract：:Spontaneous preterm birth (SPTB) is a major contributor to perinatal morbidity and mortality. However, the diagnosis of preterm labor (PTL) that leads to preterm birth is difficult, and there is a pressing need for improved diagnosis. We utilized multidimensional liquid chromatography-tandem mass spectrometry (LC/LC-M...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr0605421
更新日期：2007-04-01 00:00:00
abstract：:The deuterium, a frequently used stable isotope in isotopic labeling for quantitative proteomics, could deteriorate the accuracy and precision of proteome quantification owing to the retention time shift of deuterated peptides from the hydrogenated counterpart. We introduce a novel three-plexed peptide "diethylation" ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.8b00775
更新日期：2019-03-01 00:00:00
abstract：:Amphotericin B (AmB) is a polyene antifungal drug widely used for systemic fungal infections. In this study, a metabonomic method using gas chromatography-mass spectrometry (GC/MS) was developed to characterize the metabolic profiles of Candida albicans cells exposed to AmB. Thirty-one differentially produced metaboli...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr4002178
更新日期：2013-06-07 00:00:00
abstract：:The network of the fibrillar collagens I, III, and V, extracted from fetal calf skin and cleaved with cyanogen bromide, was studied by means of ultraviolet matrix-assisted laser desorption ionization time-of-flight mass spectrometry (UV-MALDI MS). Nearly all of the expected cyanogen bromide peptides of the different a...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr070318r
更新日期：2007-11-01 00:00:00
abstract：:We analyzed a unique rice (Oryza sativa L.) blast lesion mimic (blm) mutant for differentially expressed proteins in leaves of one- and two-week-old seedlings manifesting the lesion mimic phenotype. Gel-based one- and two-dimensional electrophoresis (1- and 2-DGE) was performed using leaves (blm and wild-type, WT) bef...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr060092c
更新日期：2006-10-01 00:00:00
abstract：:Protein oxidation and nitration have been described during spinal cord injury (SCI) in animal models. Herein, mass spectrometry unambiguously identified GDP-dissociation inhibitor-2 (GDI-2) in SCI with post-translational modifications of 3-aminotyrosine (8 h post-injury) and an acrolein adduct of GDI-2 (72 h post-inju...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr060620k
更新日期：2007-04-01 00:00:00
abstract：:Novel biomarker verification assays are urgently required to improve the efficiency of biomarker development. Benefitting from lower development costs, multiple reaction monitoring (MRM) has been used for biomarker verification as an alternative to immunoassay. However, in general MRM analysis, only one sample can be ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr4005025
更新日期：2013-09-06 00:00:00
abstract：:Frontotemporal lobar degeneration (FTLD) is an umbrella term for a heterogeneous group of young-onset dementias of uncertain prevalence and incidence worldwide. Atypical cases of FTLD with fused in sarcoma inclusions (aFTLD-U) have been described recently, but their molecular characterization is still due. Using shotg...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr2012279
更新日期：2012-04-06 00:00:00
abstract：:A metabonomic study was performed to investigate the biochemical perturbation of the serum samples from liver failure patients induced by hepatitis B virus (HBV; n=24) and control normal subjects (n=23). The serum metabonome was detected using gas chromatography-mass spectrometry (GC-MS) technique integrated with a co...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr060591d
更新日期：2007-07-01 00:00:00
abstract：:As large-scale cross-linking data becomes available, new software tools for data processing and visualization are required to replace manual data analysis. XLink-DB serves as a data storage site and visualization tool for cross-linking results. XLink-DB accepts data generated with any cross-linker and stores them in a...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr301162j
更新日期：2013-04-05 00:00:00
abstract：:Endothelial cells (ECs) form the inner layer of blood vessels and physically separate the blood from the surrounding tissue. To support tissues with nutrients and oxygen, the endothelial monolayer is semipermeable. When EC permeability is altered, blood vessels are not functional, and this is associated with disease. ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.6b00166
更新日期：2016-07-01 00:00:00
abstract：:Protein phosphorylation is a major mechanism of signal transduction in bacteria. Here, we analyzed the proteome and phosphoproteome of a wild-type strain of the food-borne pathogen Listeria monocytogenes that was grown in either chemically defined medium or rich medium containing glucose. We then compared these result...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr500929u
更新日期：2014-12-05 00:00:00
abstract：:To further our understanding of the biology of the thermophilic bacterium Geobacillus thermoleovorans T80, we now report the first proteomic analysis of the insoluble subproteome of this isolate. A combination of both shotgun and multidimensional methodologies were utilized, and a total of 8628 peptides was initially ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr0602444
更新日期：2006-09-01 00:00:00
abstract：:The interaction between the immune system and invading bacteria is sufficient to eradicate microorganisms for the majority of bacterial infections, but suppression of the microbicidal response leads to reactivation or chronic evolution of infections and to bacterial persistence. To identify the cellular pathways affec...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr200422f
更新日期：2011-09-02 00:00:00
abstract：:Searching tandem mass spectra against a peptide database requires accurate knowledge of various experimental parameters, including machine settings and details of the sample preparation protocol. In some cases, such as in reanalysis of public data sets, this experimental metadata may be missing or inaccurate. We descr...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.8b00954
更新日期：2019-04-05 00:00:00
abstract：:In recent years, proteomic data have contributed to genome annotation efforts, most notably in humans and mice, and spawned a field termed "proteogenomics". Yeast, in contrast with higher eukaryotes, has a small genome, which has lent itself to simpler ORF prediction. Despite this, continual advances in mass spectrome...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.5b00734
更新日期：2015-12-04 00:00:00
abstract：:Advances in proteomics are continually driven by the introduction of new mass spectrometric instrumentation with improved performances. The recently introduced quadrupole Orbitrap (Q Exactive) tandem mass spectrometer allows fast acquisition of high-resolution higher-energy collisional dissociation (HCD) tandem mass s...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr3000249
更新日期：2012-06-01 00:00:00
abstract：:Adipose tissue is a major storage site for lipophilic environmental contaminants. The environmental metabolic disruptor hypothesis postulates that some pollutants can promote obesity or metabolic disorders by activating nuclear receptors involved in the control of energetic homeostasis. In this context, monoethylhexyl...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr200765v
更新日期：2011-12-02 00:00:00
abstract：:Recombinant virus-like particles (VLPs) have been shown to induce protective immunity. Despite their potential significance as promising vaccine candidates, the protein composition of VLPs produced in insect cells has not been well characterized. Here we report a proteomic analysis of influenza VLPs containing hemaggl...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr200086v
更新日期：2011-08-05 00:00:00
abstract：:Hepatic fat export occurs by apolipoprotein B-100-containing lipoprotein production, whereas impaired production leads to liver steatosis. Hepatitis C virus (HCV) infection is associated to dysregulation of apoB-100 secretion and steatosis; however, the molecular mechanism by which HCV affects the apoB-100 secretion i...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr201128s
更新日期：2012-05-04 00:00:00
