Progress and Challenges in Ocean Metaproteomics and Proposed Best Practices for Data Sharing
Abstract
Ocean metaproteomics is an emerging field enabling discoveries about marine microbial communities and their impact on global biogeochemical processes. Recent ocean metaproteomic studies have provided insight into microbial nutrient transport, colimitation of carbon fixation, the metabolism of microbial biofilms, and dynamics of carbon flux in marine ecosystems. Future methodological developments could provide new capabilities such as characterizing long-term ecosystem changes, biogeochemical reaction rates, and in situ stoichiometries. Yet challenges remain for ocean metaproteomics due to the great biological diversity that produces highly complex mass spectra, as well as the difficulty in obtaining and working with environmental samples. This review summarizes the progress and challenges facing ocean metaproteomic scientists and proposes best practices for data sharing of ocean metaproteomic data sets, including the data types and metadata needed to enable intercomparisons of protein distributions and annotations that could foster global ocean metaproteomic capabilities.
- Authors:
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[1];
[3];
[1];
[1];
[4];
[5];
[6];
[7];
[1];
[4];
[1];
[8];
[9];
[10];
[1];
[1];
[11]
- Woods Hole Oceanographic Inst., Woods Hole, MA (United States)
- Dalhousie Univ., Halifax, NS (Canada)
- Univ. of Washington, Seattle, WA (United States)
- Naval Research Lab. (NRL), Washington, DC (United States)
- Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Univ. of Tennessee, Knoxville, TN (United States)
- Univ. of Minnesota, Saint Paul, MN (United States)
- College of Charleston, Charleston, SC (United States)
- Rowan Univ., Glassboro, NJ (United States)
- National Inst. of Standards and Technology (NIST), Charleston, SC (United States)
- Woods Hole Oceanographic Inst., Woods Hole, MA (United States); Univ. of Washington, Seattle, WA (United States)
- Concordia Univ., Montreal, QC (Canada)
- Publication Date:
- Research Org.:
- Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER)
- OSTI Identifier:
- 1509539
- Grant/Contract Number:
- AC05-00OR22725
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Journal of Proteome Research
- Additional Journal Information:
- Journal Volume: 18; Journal Issue: 4; Journal ID: ISSN 1535-3893
- Publisher:
- American Chemical Society (ACS)
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 54 ENVIRONMENTAL SCIENCES
Citation Formats
Saito, Mak A., Bertrand, Erin M., Duffy, Megan E., Gaylord, David A., Held, Noelle A., Hervey, William Judson, Hettich, Robert L., Jagtap, Pratik D., Janech, Michael G., Kinkade, Danie B., Leary, Dagmar H., McIlvin, Matthew R., Moore, Eli K., Morris, Robert M., Neely, Benjamin A., Nunn, Brook L., Saunders, Jaclyn K., Shepherd, Adam I., Symmonds, Nicholas I., and Walsh, David A. Progress and Challenges in Ocean Metaproteomics and Proposed Best Practices for Data Sharing. United States: N. p., 2019.
Web. doi:10.1021/acs.jproteome.8b00761.
Saito, Mak A., Bertrand, Erin M., Duffy, Megan E., Gaylord, David A., Held, Noelle A., Hervey, William Judson, Hettich, Robert L., Jagtap, Pratik D., Janech, Michael G., Kinkade, Danie B., Leary, Dagmar H., McIlvin, Matthew R., Moore, Eli K., Morris, Robert M., Neely, Benjamin A., Nunn, Brook L., Saunders, Jaclyn K., Shepherd, Adam I., Symmonds, Nicholas I., & Walsh, David A. Progress and Challenges in Ocean Metaproteomics and Proposed Best Practices for Data Sharing. United States. https://doi.org/10.1021/acs.jproteome.8b00761
Saito, Mak A., Bertrand, Erin M., Duffy, Megan E., Gaylord, David A., Held, Noelle A., Hervey, William Judson, Hettich, Robert L., Jagtap, Pratik D., Janech, Michael G., Kinkade, Danie B., Leary, Dagmar H., McIlvin, Matthew R., Moore, Eli K., Morris, Robert M., Neely, Benjamin A., Nunn, Brook L., Saunders, Jaclyn K., Shepherd, Adam I., Symmonds, Nicholas I., and Walsh, David A. Thu .
"Progress and Challenges in Ocean Metaproteomics and Proposed Best Practices for Data Sharing". United States. https://doi.org/10.1021/acs.jproteome.8b00761. https://www.osti.gov/servlets/purl/1509539.
@article{osti_1509539,
title = {Progress and Challenges in Ocean Metaproteomics and Proposed Best Practices for Data Sharing},
author = {Saito, Mak A. and Bertrand, Erin M. and Duffy, Megan E. and Gaylord, David A. and Held, Noelle A. and Hervey, William Judson and Hettich, Robert L. and Jagtap, Pratik D. and Janech, Michael G. and Kinkade, Danie B. and Leary, Dagmar H. and McIlvin, Matthew R. and Moore, Eli K. and Morris, Robert M. and Neely, Benjamin A. and Nunn, Brook L. and Saunders, Jaclyn K. and Shepherd, Adam I. and Symmonds, Nicholas I. and Walsh, David A.},
abstractNote = {Ocean metaproteomics is an emerging field enabling discoveries about marine microbial communities and their impact on global biogeochemical processes. Recent ocean metaproteomic studies have provided insight into microbial nutrient transport, colimitation of carbon fixation, the metabolism of microbial biofilms, and dynamics of carbon flux in marine ecosystems. Future methodological developments could provide new capabilities such as characterizing long-term ecosystem changes, biogeochemical reaction rates, and in situ stoichiometries. Yet challenges remain for ocean metaproteomics due to the great biological diversity that produces highly complex mass spectra, as well as the difficulty in obtaining and working with environmental samples. This review summarizes the progress and challenges facing ocean metaproteomic scientists and proposes best practices for data sharing of ocean metaproteomic data sets, including the data types and metadata needed to enable intercomparisons of protein distributions and annotations that could foster global ocean metaproteomic capabilities.},
doi = {10.1021/acs.jproteome.8b00761},
journal = {Journal of Proteome Research},
number = 4,
volume = 18,
place = {United States},
year = {Thu Jan 31 00:00:00 EST 2019},
month = {Thu Jan 31 00:00:00 EST 2019}
}
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Works referenced in this record:
Transport functions dominate the SAR11 metaproteome at low-nutrient extremes in the Sargasso Sea
journal, September 2008
- Sowell, Sarah M.; Wilhelm, Larry J.; Norbeck, Angela D.
- The ISME Journal, Vol. 3, Issue 1
Comparative metaproteomics reveals ocean-scale shifts in microbial nutrient utilization and energy transduction
journal, February 2010
- Morris, Robert M.; Nunn, Brook L.; Frazar, Christian
- The ISME Journal, Vol. 4, Issue 5
Multiple nutrient stresses at intersecting Pacific Ocean biomes detected by protein biomarkers
journal, September 2014
- Saito, M. A.; McIlvin, M. R.; Moran, D. M.
- Science, Vol. 345, Issue 6201
Metaproteomics reveals differential modes of metabolic coupling among ubiquitous oxygen minimum zone microbes
journal, July 2014
- Hawley, A. K.; Brewer, H. M.; Norbeck, A. D.
- Proceedings of the National Academy of Sciences, Vol. 111, Issue 31
Integrated metagenomic and metaproteomic analyses of marine biofilm communities
journal, November 2014
- Leary, Dagmar H.; Li, Robert W.; Hamdan, Leila J.
- Biofouling, Vol. 30, Issue 10
Protein recycling in Bering Sea algal incubations
journal, November 2014
- Moore, Ek; Harvey, Hr; Faux, Jf
- Marine Ecology Progress Series, Vol. 515
Identifying and tracking proteins through the marine water column: Insights into the inputs and preservation mechanisms of protein in sediments
journal, April 2012
- Moore, Eli K.; Nunn, Brook L.; Goodlett, David R.
- Geochimica et Cosmochimica Acta, Vol. 83
Suspended marine particulate proteins in coastal and oligotrophic waters
journal, March 2015
- Bridoux, Maxime C.; Neibauer, Jaqui; Ingalls, Anitra E.
- Journal of Marine Systems, Vol. 143
Metaproteomic analysis of a winter to spring succession in coastal northwest Atlantic Ocean microbial plankton
journal, January 2014
- Georges, Anna A.; El-Swais, Heba; Craig, Susanne E.
- The ISME Journal, Vol. 8, Issue 6
Colony formation in Phaeocystis antarctica: connecting molecular mechanisms with iron biogeochemistry
journal, January 2018
- Bender, Sara J.; Moran, Dawn M.; McIlvin, Matthew R.
- Biogeosciences, Vol. 15, Issue 16
Methionine synthase interreplacement in diatom cultures and communities: Implications for the persistence of B 12 use by eukaryotic phytoplankton
journal, June 2013
- Bertrand, Erin M.; Moran, Dawn M.; McIlvin, Matthew R.
- Limnology and Oceanography, Vol. 58, Issue 4
Evaluation of electrophoretic protein extraction and database-driven protein identification from marine sediments: Protein identification in sediments
journal, May 2012
- Moore, Eli K.; Nunn, Brook L.; Faux, Jessica F.
- Limnology and Oceanography: Methods, Vol. 10, Issue 5
Needles in the blue sea: Sub‐species specificity in targeted protein biomarker analyses within the vast oceanic microbial metaproteome
journal, July 2015
- Saito, Mak A.; Dorsk, Alexander; Post, Anton F.
- PROTEOMICS, Vol. 15, Issue 20
A metaproteomic assessment of winter and summer bacterioplankton from Antarctic Peninsula coastal surface waters
journal, April 2012
- Williams, Timothy J.; Long, Emilie; Evans, Flavia
- The ISME Journal, Vol. 6, Issue 10
Influence of cobalamin scarcity on diatom molecular physiology and identification of a cobalamin acquisition protein
journal, May 2012
- Bertrand, E. M.; Allen, A. E.; Dupont, C. L.
- Proceedings of the National Academy of Sciences, Vol. 109, Issue 26
The Transcriptome and Proteome of the Diatom Thalassiosira pseudonana Reveal a Diverse Phosphorus Stress Response
journal, March 2012
- Dyhrman, Sonya T.; Jenkins, Bethany D.; Rynearson, Tatiana A.
- PLoS ONE, Vol. 7, Issue 3
Divergent responses of Atlantic coastal and oceanic Synechococcus to iron limitation
journal, July 2015
- Mackey, Katherine R. M.; Post, Anton F.; McIlvin, Matthew R.
- Proceedings of the National Academy of Sciences, Vol. 112, Issue 32
Proteome Changes Driven by Phosphorus Deficiency and Recovery in the Brown Tide-Forming Alga Aureococcus anophagefferens
journal, December 2011
- Wurch, Louie L.; Bertrand, Erin M.; Saito, Mak A.
- PLoS ONE, Vol. 6, Issue 12
Physiology, Fe(II) oxidation, and Fe mineral formation by a marine planktonic cyanobacterium grown under ferruginous conditions
journal, October 2015
- Swanner, Elizabeth D.; Wu, Wenfang; Hao, Likai
- Frontiers in Earth Science, Vol. 3
Deciphering diatom biochemical pathways via whole-cell proteomics
journal, June 2009
- Nunn, Bl; Aker, Jr; Shaffer, Sa
- Aquatic Microbial Ecology, Vol. 55
Proteomics of C olwellia psychrerythraea at subzero temperatures - a life with limited movement, flexible membranes and vital DNA repair : Proteomics of microbes at subzero temperatures
journal, February 2015
- Nunn, Brook L.; Slattery, Krystal V.; Cameron, Karen A.
- Environmental Microbiology, Vol. 17, Issue 7
Challenges and perspectives of metaproteomic data analysis
journal, November 2017
- Heyer, Robert; Schallert, Kay; Zoun, Roman
- Journal of Biotechnology, Vol. 261
Examination of Microbial Proteome Preservation Techniques Applicable to Autonomous Environmental Sample Collection
journal, January 2011
- Saito, Mak A.; Bulygin, Vladimir V.; Moran, Dawn M.
- Frontiers in Microbiology, Vol. 2
A precision multi-sampler for deep-sea hydrothermal microbial mat studies
journal, December 2012
- Breier, J. A.; Gomez-Ibanez, D.; Reddington, E.
- Deep Sea Research Part I: Oceanographic Research Papers, Vol. 70
Iron, manganese, and lead at Hawaii Ocean Time-series station ALOHA: Temporal variability and an intermediate water hydrothermal plume
journal, February 2005
- Boyle, Edward A.; Bergquist, Bridget A.; Kayser, Richard A.
- Geochimica et Cosmochimica Acta, Vol. 69, Issue 4
Organic matter processing by microbial communities throughout the Atlantic water column as revealed by metaproteomics
journal, December 2017
- Bergauer, Kristin; Fernandez-Guerra, Antonio; Garcia, Juan A. L.
- Proceedings of the National Academy of Sciences, Vol. 115, Issue 3
Environmental Genome Shotgun Sequencing of the Sargasso Sea
journal, April 2004
- Venter, J. C.
- Science, Vol. 304, Issue 5667
Community Genomics Among Stratified Microbial Assemblages in the Ocean's Interior
journal, January 2006
- DeLong, E. F.
- Science, Vol. 311, Issue 5760
A comparison of non-hydrolytic methods for extracting amino acids and proteins from coastal marine sediments
journal, January 2006
- Nunn, Brook L.; Keil, Richard G.
- Marine Chemistry, Vol. 98, Issue 1
Mineralogical and textural controls on the organic composition of coastal marine sediments: Hydrodynamic separation using SPLITT-fractionation
journal, January 1994
- Keil, Richard G.; Tsamakis, Elizabeth; Fuh, C. Bor
- Geochimica et Cosmochimica Acta, Vol. 58, Issue 2
Community Proteomics of a Natural Microbial Biofilm
journal, June 2005
- Ram, Rachna J.; VerBerkmoes, Nathan C.; Thelen, Michael P.
- Science, Vol. 308, Issue 5730
Evaluation of “Shotgun” Proteomics for Identification of Biological Threat Agents in Complex Environmental Matrixes: Experimental Simulations
journal, February 2005
- VerBerkmoes, Nathan C.; Hervey, W. Judson; Shah, Manesh
- Analytical Chemistry, Vol. 77, Issue 3
Sulfur oxidizers dominate carbon fixation at a biogeochemical hot spot in the dark ocean
journal, July 2013
- Mattes, Timothy E.; Nunn, Brook L.; Marshall, Katharine T.
- The ISME Journal, Vol. 7, Issue 12
Computational Methods for Understanding Mass Spectrometry–Based Shotgun Proteomics Data
journal, July 2018
- Sinitcyn, Pavel; Rudolph, Jan Daniel; Cox, Jürgen
- Annual Review of Biomedical Data Science, Vol. 1, Issue 1
Targeted Data Extraction of the MS/MS Spectra Generated by Data-independent Acquisition: A New Concept for Consistent and Accurate Proteome Analysis
journal, January 2012
- Gillet, Ludovic C.; Navarro, Pedro; Tate, Stephen
- Molecular & Cellular Proteomics, Vol. 11, Issue 6
Technical considerations for large-scale parallel reaction monitoring analysis
journal, April 2014
- Gallien, Sebastien; Bourmaud, Adele; Kim, Sang Yoon
- Journal of Proteomics, Vol. 100
Targeted Proteomic Quantification on Quadrupole-Orbitrap Mass Spectrometer
journal, September 2012
- Gallien, Sebastien; Duriez, Elodie; Crone, Catharina
- Molecular & Cellular Proteomics, Vol. 11, Issue 12
Selected reaction monitoring applied to proteomics
journal, March 2011
- Gallien, Sebastien; Duriez, Elodie; Domon, Bruno
- Journal of Mass Spectrometry, Vol. 46, Issue 3
MZmine 2: Modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data
journal, July 2010
- Pluskal, Tomáš; Castillo, Sandra; Villar-Briones, Alejandro
- BMC Bioinformatics, Vol. 11, Issue 1
Diatom Proteomics Reveals Unique Acclimation Strategies to Mitigate Fe Limitation
journal, October 2013
- Nunn, Brook L.; Faux, Jessica F.; Hippmann, Anna A.
- PLoS ONE, Vol. 8, Issue 10
CharmeRT: Boosting Peptide Identifications by Chimeric Spectra Identification and Retention Time Prediction
journal, June 2018
- Dorfer, Viktoria; Maltsev, Sergey; Winkler, Stephan
- Journal of Proteome Research, Vol. 17, Issue 8
Intercalibration in chemical oceanography-Getting the right number: Intercalibration in chemical oceanography
journal, January 2013
- Cutter, Gregory A.
- Limnology and Oceanography: Methods, Vol. 11, Issue 7
How to talk about protein‐level false discovery rates in shotgun proteomics
journal, September 2016
- The, Matthew; Tasnim, Ayesha; Käll, Lukas
- PROTEOMICS, Vol. 16, Issue 18
Mass spectrometrists should search only for peptides they care about
journal, June 2015
- Noble, William Stafford
- Nature Methods, Vol. 12, Issue 7
Protein inference: a review
journal, February 2012
- Huang, T.; Wang, J.; Yu, W.
- Briefings in Bioinformatics, Vol. 13, Issue 5
Interpretation of Shotgun Proteomic Data: The Protein Inference Problem
journal, July 2005
- Nesvizhskii, Alexey I.; Aebersold, Ruedi
- Molecular & Cellular Proteomics, Vol. 4, Issue 10
Shotgun proteomics aids discovery of novel protein-coding genes, alternative splicing, and "resurrected" pseudogenes in the mouse genome
journal, April 2011
- Brosch, M.; Saunders, G. I.; Frankish, A.
- Genome Research, Vol. 21, Issue 5
An update on LNCipedia: a database for annotated human lncRNA sequences
journal, March 2015
- Volders, P. J.; Verheggen, K.; Menschaert, G.
- Nucleic Acids Research, Vol. 43, Issue 8
Peptidomic discovery of short open reading frame–encoded peptides in human cells
journal, November 2012
- Slavoff, Sarah A.; Mitchell, Andrew J.; Schwaid, Adam G.
- Nature Chemical Biology, Vol. 9, Issue 1
Navigating through metaproteomics data: A logbook of database searching
journal, April 2015
- Muth, Thilo; Kolmeder, Carolin A.; Salojärvi, Jarkko
- PROTEOMICS, Vol. 15, Issue 20
Critical decisions in metaproteomics: achieving high confidence protein annotations in a sea of unknowns
journal, November 2016
- Timmins-Schiffman, Emma; May, Damon H.; Mikan, Molly
- The ISME Journal, Vol. 11, Issue 2
Substrate-Controlled Succession of Marine Bacterioplankton Populations Induced by a Phytoplankton Bloom
journal, May 2012
- Teeling, H.; Fuchs, B. M.; Becher, D.
- Science, Vol. 336, Issue 6081
Metaproteomics of aquatic microbial communities in a deep and stratified estuary
journal, September 2015
- Colatriano, David; Ramachandran, Arthi; Yergeau, Etienne
- PROTEOMICS, Vol. 15, Issue 20
Species-Level Deconvolution of Metagenome Assemblies with Hi-C–Based Contact Probability Maps
journal, May 2014
- Burton, Joshua N.; Liachko, Ivan; Dunham, Maitreya J.
- G3: Genes|Genomes|Genetics, Vol. 4, Issue 7
Single-Cell Genomics Reveals Hundreds of Coexisting Subpopulations in Wild Prochlorococcus
journal, April 2014
- Kashtan, N.; Roggensack, S. E.; Rodrigue, S.
- Science, Vol. 344, Issue 6182
Characterization of Prochlorococcus clades from iron-depleted oceanic regions
journal, August 2010
- Rusch, D. B.; Martiny, A. C.; Dupont, C. L.
- Proceedings of the National Academy of Sciences, Vol. 107, Issue 37
The Sorcerer II Global Ocean Sampling Expedition: Expanding the Universe of Protein Families
journal, March 2007
- Yooseph, Shibu; Sutton, Granger; Rusch, Douglas B.
- PLoS Biology, Vol. 5, Issue 3
Quantitative Proteomics Analysis Demonstrates Post-transcriptional Regulation of Embryonic Stem Cell Differentiation to Hematopoiesis
journal, November 2007
- Williamson, Andrew J. K.; Smith, Duncan L.; Blinco, David
- Molecular & Cellular Proteomics, Vol. 7, Issue 3
The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): Illuminating the Functional Diversity of Eukaryotic Life in the Oceans through Transcriptome Sequencing
journal, June 2014
- Keeling, Patrick J.; Burki, Fabien; Wilcox, Heather M.
- PLoS Biology, Vol. 12, Issue 6
An Alignment-Free “Metapeptide” Strategy for Metaproteomic Characterization of Microbiome Samples Using Shotgun Metagenomic Sequencing
journal, July 2016
- May, Damon H.; Timmins-Schiffman, Emma; Mikan, Molly P.
- Journal of Proteome Research, Vol. 15, Issue 8
Genomes of diverse isolates of the marine cyanobacterium Prochlorococcus
journal, September 2014
- Biller, Steven J.; Berube, Paul M.; Berta-Thompson, Jessie W.
- Scientific Data, Vol. 1, Issue 1
Genomic and proteomic characterization of “ Candidatus Nitrosopelagicus brevis”: An ammonia-oxidizing archaeon from the open ocean
journal, January 2015
- Santoro, Alyson E.; Dupont, Christopher L.; Richter, R. Alex
- Proceedings of the National Academy of Sciences, Vol. 112, Issue 4
An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database
journal, November 1994
- Eng, Jimmy K.; McCormack, Ashley L.; Yates, John R.
- Journal of the American Society for Mass Spectrometry, Vol. 5, Issue 11
Comet: An open-source MS/MS sequence database search tool
journal, December 2012
- Eng, Jimmy K.; Jahan, Tahmina A.; Hoopmann, Michael R.
- PROTEOMICS, Vol. 13, Issue 1
A method for reducing the time required to match protein sequences with tandem mass spectra
journal, January 2003
- Craig, Robertson; Beavis, Ronald C.
- Rapid Communications in Mass Spectrometry, Vol. 17, Issue 20
Deep metaproteomic analysis of human salivary supernatant
journal, April 2012
- Jagtap, Pratik; McGowan, Thomas; Bandhakavi, Sricharan
- PROTEOMICS, Vol. 12, Issue 7
A two-step database search method improves sensitivity in peptide sequence matches for metaproteomics and proteogenomics studies
journal, March 2013
- Jagtap, Pratik; Goslinga, Jill; Kooren, Joel A.
- PROTEOMICS, Vol. 13, Issue 8
Flexible and Accessible Workflows for Improved Proteogenomic Analysis Using the Galaxy Framework
journal, October 2014
- Jagtap, Pratik D.; Johnson, James E.; Onsongo, Getiria
- Journal of Proteome Research, Vol. 13, Issue 12
Metaproteomic analysis using the Galaxy framework
journal, July 2015
- Jagtap, Pratik D.; Blakely, Alan; Murray, Kevin
- PROTEOMICS, Vol. 15, Issue 20
Protein relative abundance patterns associated with sucrose-induced dysbiosis are conserved across taxonomically diverse oral microcosm biofilm models of dental caries
journal, December 2015
- Rudney, Joel D.; Jagtap, Pratik D.; Reilly, Cavan S.
- Microbiome, Vol. 3, Issue 1
Tandem Mass Spectrum Identification via Cascaded Search
journal, June 2015
- Kertesz-Farkas, Attila; Keich, Uri; Noble, William Stafford
- Journal of Proteome Research, Vol. 14, Issue 8
PeptideShaker enables reanalysis of MS-derived proteomics data sets
journal, January 2015
- Vaudel, Marc; Burkhart, Julia M.; Zahedi, René P.
- Nature Biotechnology, Vol. 33, Issue 1
A Potential Golden Age to Come-Current Tools, Recent Use Cases, and Future Avenues for De Novo Sequencing in Proteomics
journal, August 2018
- Muth, Thilo; Hartkopf, Felix; Vaudel, Marc
- PROTEOMICS, Vol. 18, Issue 18
The unique peptidome: Taxon-specific tryptic peptides as biomarkers for targeted metaproteomics
journal, August 2016
- Mesuere, Bart; Van der Jeugt, Felix; Devreese, Bart
- PROTEOMICS, Vol. 16, Issue 17
Unipept: Tryptic Peptide-Based Biodiversity Analysis of Metaproteome Samples
journal, October 2012
- Mesuere, Bart; Devreese, Bart; Debyser, Griet
- Journal of Proteome Research, Vol. 11, Issue 12
Unipept web services for metaproteomics analysis
journal, January 2016
- Mesuere, Bart; Willems, Toon; Van der Jeugt, Felix
- Bioinformatics, Vol. 32, Issue 11
MPA Portable: A Stand-Alone Software Package for Analyzing Metaproteome Samples on the Go
journal, December 2017
- Muth, Thilo; Kohrs, Fabian; Heyer, Robert
- Analytical Chemistry, Vol. 90, Issue 1
MetaGOmics: A Web-Based Tool for Peptide-Centric Functional and Taxonomic Analysis of Metaproteomics Data
journal, December 2017
- Riffle, Michael; May, Damon; Timmins-Schiffman, Emma
- Proteomes, Vol. 6, Issue 1
Unipept 4.0: Functional Analysis of Metaproteome Data
journal, November 2018
- Gurdeep Singh, Robbert; Tanca, Alessandro; Palomba, Antonio
- Journal of Proteome Research, Vol. 18, Issue 2
MEGAN analysis of metagenomic data
journal, February 2007
- Huson, D. H.; Auch, A. F.; Qi, J.
- Genome Research, Vol. 17, Issue 3
Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper
journal, April 2017
- Huerta-Cepas, Jaime; Forslund, Kristoffer; Coelho, Luis Pedro
- Molecular Biology and Evolution, Vol. 34, Issue 8
Annotation Error in Public Databases: Misannotation of Molecular Function in Enzyme Superfamilies
journal, December 2009
- Schnoes, Alexandra M.; Brown, Shoshana D.; Dodevski, Igor
- PLoS Computational Biology, Vol. 5, Issue 12
Carbonate-sensitive phytotransferrin controls high-affinity iron uptake in diatoms
journal, March 2018
- McQuaid, Jeffrey B.; Kustka, Adam B.; Oborník, Miroslav
- Nature, Vol. 555, Issue 7697
A large-scale evaluation of computational protein function prediction
journal, January 2013
- Radivojac, Predrag; Clark, Wyatt T.; Oron, Tal Ronnen
- Nature Methods, Vol. 10, Issue 3
Iron Stress in Open-Ocean Cyanobacteria ( Synechococcus , Trichodesmium , and Crocosphaera spp.): Identification of the IdiA Protein
journal, December 2001
- Webb, E. A.; Moffett, J. W.; Waterbury, J. B.
- Applied and Environmental Microbiology, Vol. 67, Issue 12
SemantEco: A semantically powered modular architecture for integrating distributed environmental and ecological data
journal, July 2014
- Patton, Evan W.; Seyed, Patrice; Wang, Ping
- Future Generation Computer Systems, Vol. 36
PRIDE: The proteomics identifications database
journal, August 2005
- Martens, Lennart; Hermjakob, Henning; Jones, Philip
- PROTEOMICS, Vol. 5, Issue 13
Calibration Using a Single-Point External Reference Material Harmonizes Quantitative Mass Spectrometry Proteomics Data between Platforms and Laboratories
journal, October 2018
- Pino, Lindsay K.; Searle, Brian C.; Huang, Eric L.
- Analytical Chemistry, Vol. 90, Issue 21
Niche Partitioning Among Prochlorococcus Ecotypes Along Ocean-Scale Environmental Gradients
journal, March 2006
- Johnson, Z. I.
- Science, Vol. 311, Issue 5768
The Potential Cost of High-Throughput Proteomics
journal, February 2011
- White, F. M.
- Science Signaling, Vol. 4, Issue 160
The Growing Human Footprint on Coastal and Open-Ocean Biogeochemistry
journal, June 2010
- Doney, S. C.
- Science, Vol. 328, Issue 5985
Works referencing / citing this record:
Challenges and promise at the interface of metaproteomics and genomics: an overview of recent progress in metaproteogenomic data analysis
journal, April 2019
- Schiebenhoefer, Henning; Van Den Bossche, Tim; Fuchs, Stephan
- Expert Review of Proteomics, Vol. 16, Issue 5
Cyanobacteria and cyanophage contributions to carbon and nitrogen cycling in an oligotrophic oxygen-deficient zone
journal, June 2019
- Fuchsman, Clara A.; Palevsky, Hilary I.; Widner, Brittany
- The ISME Journal, Vol. 13, Issue 11
Deciphering the Functioning of Microbial Communities: Shedding Light on the Critical Steps in Metaproteomics
journal, October 2019
- Géron, Augustin; Werner, Johannes; Wattiez, Ruddy
- Frontiers in Microbiology, Vol. 10
Bacterioplankton reveal years-long retention of Atlantic deep-ocean water by the Tropic Seamount
journal, March 2020
- Giljan, Greta; Kamennaya, Nina A.; Otto, Andreas
- Scientific Reports, Vol. 10, Issue 1