Addressing the challenge of soil metaproteome complexity by improving metaproteome depth of coverage through two-dimensional liquid chromatography

[1]  Christopher V. Rao,et al.  Ancient Regulatory Role of Lysine Acetylation in Central Metabolism , 2017, mBio.

[2]  L. Paša-Tolić,et al.  Quantitative iTRAQ-based secretome analysis reveals species-specific and temporal shifts in carbon utilization strategies among manganese(II)-oxidizing Ascomycete fungi. , 2017, Fungal genetics and biology : FG & B.

[3]  E. Nicolás,et al.  Ecological and functional adaptations to water management in a semiarid agroecosystem: a soil metaproteomics approach , 2017, Scientific Reports.

[4]  R. Hettich,et al.  Optimized Extraction Method To Remove Humic Acid Interferences from Soil Samples Prior to Microbial Proteome Measurements. , 2017, Journal of proteome research.

[5]  Michael Wagner,et al.  Capturing the genetic makeup of the active microbiome in situ , 2017, The ISME Journal.

[6]  S. Fuchs,et al.  Microbial functionality as affected by experimental warming of a temperate mountain forest soil—A metaproteomics survey , 2017 .

[7]  B. Montanini,et al.  A metaproteomic approach dissecting major bacterial functions in the rhizosphere of plants living in serpentine soil , 2017, Analytical and Bioanalytical Chemistry.

[8]  Cathy H. Wu,et al.  UniProt: the Universal Protein knowledgebase , 2004, Nucleic Acids Res..

[9]  A. Simao-Beaunoir,et al.  Proteome Analyses of Soil Bacteria Grown in the Presence of Potato Suberin, a Recalcitrant Biopolymer , 2016, Microbes and environments.

[10]  N. Jehmlich,et al.  The active microbial diversity drives ecosystem multifunctionality and is physiologically related to carbon availability in Mediterranean semi‐arid soils , 2016, Molecular ecology.

[11]  B. Henrissat,et al.  Comparative Analysis of Secretome Profiles of Manganese(II)-Oxidizing Ascomycete Fungi , 2016, PloS one.

[12]  A. Zemla,et al.  Light Regimes Shape Utilization of Extracellular Organic C and N in a Cyanobacterial Biofilm , 2016, mBio.

[13]  Sarah J. Fansler,et al.  Moleculo Long-Read Sequencing Facilitates Assembly and Genomic Binning from Complex Soil Metagenomes , 2016, mSystems.

[14]  P. Bonfante,et al.  Soil metaproteomics reveals an inter-kingdom stress response to the presence of black truffles , 2016, Scientific Reports.

[15]  Kristin E. Burnum-Johnson,et al.  MPLEx: a Robust and Universal Protocol for Single-Sample Integrative Proteomic, Metabolomic, and Lipidomic Analyses , 2016, mSystems.

[16]  I. Baldwin,et al.  Bacteria dominate the short-term assimilation of plant-derived N in soil , 2016 .

[17]  J. Jansson,et al.  A multi-omic future for microbiome studies , 2016, Nature Microbiology.

[18]  H. Heipieper,et al.  In situ protein-SIP highlights Burkholderiaceae as key players degrading toluene by para ring hydroxylation in a constructed wetland model. , 2016, Environmental microbiology.

[19]  N. Jehmlich,et al.  The ecological and physiological responses of the microbial community from a semiarid soil to hydrocarbon contamination and its bioremediation using compost amendment. , 2016, Journal of proteomics.

[20]  Uma Kota,et al.  Improving Proteome Coverage by Reducing Sample Complexity via Chromatography. , 2016, Advances in experimental medicine and biology.

[21]  Meagan C. Burnet,et al.  Evaluating Models of Cellulose Degradation by Fibrobacter succinogenes S85 , 2015, PloS one.

[22]  J. Prosser.  Dispersing misconceptions and identifying opportunities for the use of 'omics' in soil microbial ecology , 2015, Nature Reviews Microbiology.

[23]  Mark P. Waldrop,et al.  Multi-omics of permafrost, active layer and thermokarst bog soil microbiomes , 2015, Nature.

[24]  Itai Sharon,et al.  Metabolic interdependencies between phylogenetically novel fermenters and respiratory organisms in an unconfined aquifer , 2014, The ISME Journal.

[25]  F. Bastida,et al.  Metaproteomics of soils from semiarid environment: functional and phylogenetic information obtained with different protein extraction methods. , 2014, Journal of proteomics.

[26]  E. Blagodatskaya,et al.  Active microorganisms in soil: Critical review of estimation criteria and approaches , 2013 .

[27]  Jörg Bernhardt,et al.  Metaproteomics to unravel major microbial players in leaf litter and soil environments: Challenges and perspectives , 2013, Proteomics.

[28]  Stephen J. Callister,et al.  Characterizing microbial community and geochemical dynamics at hydrothermal vents using osmotically driven continuous fluid samplers. , 2013, Environmental science & technology.

[29]  Emanuel Schmid,et al.  Soil metaproteomics – Comparative evaluation of protein extraction protocols , 2012, Soil biology & biochemistry.

[30]  Paul D Piehowski,et al.  Metagenomic and metaproteomic insights into bacterial communities in leaf-cutter ant fungus gardens , 2012, The ISME Journal.

[31]  Ronald J Moore,et al.  Simple sodium dodecyl sulfate-assisted sample preparation method for LC-MS-based proteomics applications. , 2012, Analytical chemistry.

[32]  Ronald J. Moore,et al.  Reversed‐phase chromatography with multiple fraction concatenation strategy for proteome profiling of human MCF10A cells , 2011, Proteomics.

[33]  O. Ogunseitan,et al.  Molecular analyses of β-glucosidase diversity and function in soil , 2011 .

[34]  Philip Hugenholtz,et al.  Proteome insights into the symbiotic relationship between a captive colony of Nasutitermes corniger and its hindgut microbiome , 2011, The ISME Journal.

[35]  Stephen J. Callister,et al.  Analysis of biostimulated microbial communities from two field experiments reveals temporal and spatial differences in proteome profiles. , 2010, Environmental science & technology.

[36]  Eoin L. Brodie,et al.  Direct cellular lysis/protein extraction protocol for soil metaproteomics. , 2010, Journal of proteome research.

[37]  E. Taylor,et al.  Microbial Protein in Soil: Influence of Extraction Method and C Amendment on Extraction and Recovery , 2010, Microbial Ecology.

[38]  Gordon A. Anderson,et al.  DtaRefinery, a Software Tool for Elimination of Systematic Errors from Parent Ion Mass Measurements in Tandem Mass Spectra Data Sets* , 2009, Molecular & Cellular Proteomics.

[39]  F. Bastida,et al.  Soil metaproteomics: a review of an emerging environmental science. Significance, methodology and perspectives , 2009 .

[40]  Kenneth H. Williams,et al.  Proteogenomic Monitoring of Geobacter Physiology during Stimulated Uranium Bioremediation , 2009, Applied and Environmental Microbiology.

[41]  P. Pevzner,et al.  False discovery rates of protein identifications: a strike against the two-peptide rule. , 2009, Journal of proteome research.

[42]  M. Mann,et al.  Universal sample preparation method for proteome analysis , 2009, Nature Methods.

[43]  Dwight R Stoll,et al.  Equation for peak capacity estimation in two-dimensional liquid chromatography. , 2009, Analytical chemistry.

[44]  P. Pevzner,et al.  Spectral probabilities and generating functions of tandem mass spectra: a strike against decoy databases. , 2008, Journal of proteome research.

[45]  Navdeep Jaitly,et al.  DeconMSn: a software tool for accurate parent ion monoisotopic mass determination for tandem mass spectra , 2008, Bioinform..

[46]  E. Heinzle,et al.  Two-dimensional reversed-phase x ion-pair reversed-phase HPLC: an alternative approach to high-resolution peptide separation for shotgun proteome analysis. , 2007, Journal of proteome research.

[47]  M. Washburn,et al.  Multidimensional separations-based shotgun proteomics. , 2007, Chemical reviews.

[48]  Laura E. Green,et al.  The role of ecological theory in microbial ecology , 2007, Nature Reviews Microbiology.

[49]  Steven P Gygi,et al.  Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry , 2007, Nature Methods.

[50]  L. Ranjard,et al.  Metaproteomics: A New Approach for Studying Functional Microbial Ecology , 2007, Microbial Ecology.

[51]  Ronald J Moore,et al.  Chemically etched open tubular and monolithic emitters for nanoelectrospray ionization mass spectrometry. , 2006, Analytical chemistry.

[52]  Michael P Washburn,et al.  Proteomic analysis by multidimensional protein identification technology. , 2006, Methods in molecular biology.

[53]  J. Jansson,et al.  Combined bromodeoxyuridine immunocapture and terminal-restriction fragment length polymorphism analysis highlights differences in the active soil bacterial metagenome due to Glomus mosseae inoculation or plant species. , 2005, Environmental microbiology.

[54]  J. Rappsilber,et al.  Self‐made frits for nanoscale columns in proteomics , 2005, Proteomics.

[55]  J. Gebler,et al.  Orthogonality of separation in two-dimensional liquid chromatography. , 2005, Analytical chemistry.

[56]  P. Taylor.  Matrix effects: the Achilles heel of quantitative high-performance liquid chromatography-electrospray-tandem mass spectrometry. , 2005, Clinical biochemistry.

[57]  Jianwu Tang,et al.  How soil moisture, rain pulses, and growth alter the response of ecosystem respiration to temperature , 2004 .

[58]  Cathy H. Wu,et al.  UniProt: the Universal Protein knowledgebase , 2004, Nucleic Acids Res..

[59]  Joshua E. Elias,et al.  Evaluation of multidimensional chromatography coupled with tandem mass spectrometry (LC/LC-MS/MS) for large-scale protein analysis: the yeast proteome. , 2003, Journal of proteome research.

[60]  R. Bischoff,et al.  An automated on-line multidimensional HPLC system for protein and peptide mapping with integrated sample preparation. , 2002, Analytical chemistry.

[61]  J. Yates,et al.  An automated multidimensional protein identification technology for shotgun proteomics. , 2001, Analytical chemistry.

[62]  J. Yates,et al.  Large-scale analysis of the yeast proteome by multidimensional protein identification technology , 2001, Nature Biotechnology.

[63]  J. Giddings.  Two-dimensional separations: concept and promise. , 1984, Analytical chemistry.

[64]  C. Horváth,et al.  Peak capacity in chromatography , 1967 .

[65]  J. Folch,et al.  Preparation of lipide extracts from brain tissue. , 1951, The Journal of biological chemistry.