@article{hinzke_kouris_hughes_strous_kleiner_2019, title={More Is Not Always Better: Evaluation of 1D and 2D-LC-MS/MS Methods for Metaproteomics}, volume={10}, ISSN={["1664-302X"]}, DOI={10.3389/fmicb.2019.00238}, abstractNote={Metaproteomics, the study of protein expression in microbial communities, is a versatile tool for environmental microbiology. Achieving sufficiently high metaproteome coverage to obtain a comprehensive picture of the activities and interactions in microbial communities is one of the current challenges in metaproteomics. An essential step to maximize the number of identified proteins is peptide separation via liquid chromatography (LC) prior to mass spectrometry (MS). Thorough optimization and comparison of LC methods for metaproteomics are, however, currently lacking. Here, we present an extensive development and test of different 1D and 2D-LC approaches for metaproteomic peptide separations. We used fully characterized mock community samples to evaluate metaproteomic approaches with very long analytical columns (50 and 75 cm) and long gradients (up to 12 h). We assessed a total of over 20 different 1D and 2D-LC approaches in terms of number of protein groups and unique peptides identified, peptide spectrum matches (PSMs) generated, the ability to detect proteins of low-abundance species, the effect of technical replicate runs on protein identifications and method reproducibility. We show here that, while 1D-LC approaches are faster and easier to set up and lead to more identifications per minute of runtime, 2D-LC approaches allow for a higher overall number of identifications with up to >10,000 protein groups identified. We also compared the 1D and 2D-LC approaches to a standard GeLC workflow, in which proteins are pre-fractionated via gel electrophoresis. This method yielded results comparable to the 2D-LC approaches, however with the drawback of a much increased sample preparation time. Based on our results, we provide recommendations on how to choose the best LC approach for metaproteomics experiments, depending on the study aims.}, journal={FRONTIERS IN MICROBIOLOGY}, author={Hinzke, Tjorven and Kouris, Angela and Hughes, Rebecca-Ayme and Strous, Marc and Kleiner, Manuel}, year={2019}, month={Feb} }
 @article{hughes_jin_zhang_zhang_tran_williams_lindsey_miller_2018, title={Genome sequence, metabolic properties and cyanobacterial attachment of Porphyrobacter sp. HT-58-2 isolated from a filamentous cyanobacterium–microbial consortium}, volume={164}, ISSN={1350-0872 1465-2080}, url={http://dx.doi.org/10.1099/mic.0.000706}, DOI={10.1099/mic.0.000706}, abstractNote={Tolyporphins are structurally diverse tetrapyrrole macrocycles produced by the cyanobacterial culture HT-58-2. Although tolyporphins were discovered over 25 years ago, little was known about the microbiology of the culture. The studies reported herein expand the description of the community of predominantly alphaproteobacteria associated with the filamentous HT-58-2 cyanobacterium and isolate a dominant bacterium, Porphyrobacter sp. HT-58-2, for which the complete genome is established and growth properties are examined. Fluorescence in situ hybridization (FISH) analysis of the cyanobacterium-microbial community with a probe targeting the 16S rRNA of Porphyrobacter sp. HT-58-2 showed fluorescence emanating from the cyanobacterial sheath. Although genes for the biosynthesis of bacteriochlorophyll a (BChl a) are present in the Porphyrobacter sp. HT-58-2 genome, the pigment was not detected under the conditions examined, implying the absence of phototrophic growth. Comparative analysis of four Porphyrobacter spp. genomes from worldwide collection sites showed significant collinear gene blocks, with two inversions and three deletion regions. Taken together, the results enrich our understanding of the HT-58-2 cyanobacterium-microbial culture.}, number={10}, journal={Microbiology}, publisher={Microbiology Society}, author={Hughes, Rebecca-Ayme and Jin, Xiaohe and Zhang, Yunlong and Zhang, Ran and Tran, Sabrina and Williams, Philip G. and Lindsey, Jonathan S. and Miller, Eric S.}, year={2018}, month={Oct}, pages={1229–1239} }
 @article{hughes_zhang_zhang_williams_lindsey_miller_2017, title={Genome Sequence and Composition of a Tolyporphin-Producing Cyanobacterium-Microbial Community}, volume={83}, ISSN={["1098-5336"]}, DOI={10.1128/aem.01068-17}, abstractNote={ABSTRACT}, number={19}, journal={APPLIED AND ENVIRONMENTAL MICROBIOLOGY}, author={Hughes, Rebecca-Ayme and Zhang, Yunlong and Zhang, Ran and Williams, Philip G. and Lindsey, Jonathan S. and Miller, Eric S.}, year={2017}, month={Oct} }
 @article{zhang_zhang_hughes_dai_gurr_williams_miller_lindsey_2017, title={Quantitation of Tolyporphins, Diverse Tetrapyrrole Secondary Metabolites with Chlorophyll-Like Absorption, from a Filamentous Cyanobacterium-Microbial Community}, volume={29}, ISSN={0958-0344}, url={http://dx.doi.org/10.1002/pca.2735}, DOI={10.1002/pca.2735}, abstractNote={Abstract}, number={2}, journal={Phytochemical Analysis}, publisher={Wiley}, author={Zhang, Yunlong and Zhang, Ran and Hughes, Rebecca-Ayme and Dai, Jingqiu and Gurr, Joshua R. and Williams, Philip G. and Miller, Eric S. and Lindsey, Jonathan S.}, year={2017}, month={Nov}, pages={205–216} }