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References from Current progress and critical challenges to overcome in the bioinformatics of mass spectrometry-based metaproteomics. Local targets link to admitted publications; unresolved targets remain external evidence.
10.1111/j.1462-2920.2004.00687.x
10.1111/j.1462-2920.2004.00687.x · External reference
10.1016/j.jprot.2020.103737
10.1016/j.jprot.2020.103737 · External reference
10.1038/ismej.2008.108
10.1038/ismej.2008.108 · External reference
10.3390/proteomes7010002
10.3390/proteomes7010002 · External reference
Metaproteomics of the human gut microbiota: challenges and contributions to other OMICS
10.1016/j.clinms.2019.06.001 · 2019 · External reference
10.1080/19490976.2020.1755413
10.1080/19490976.2020.1755413 · External reference
Deep metaproteomic analysis of human salivary supernatant
10.1002/pmic.201100503 · 2012 · External reference
Metaproteome and metabolome of oral microbial communities
10.1111/prd.12351 · 2020 · External reference
10.1016/j.tim.2005.12.006
10.1016/j.tim.2005.12.006 · External reference
A community-supported metaproteomic pipeline for improving peptide identifications in hydrothermal vent microbiota
10.1093/bib/bbab052 · 2021 · External reference
10.3390/molecules26082299
10.3390/molecules26082299 · External reference
Genomics as a potential tool to unravel the rhizosphere microbiome interactions on plant health
10.1016/j.mimet.2021.106215 · 2021 · External reference
Functional metaproteomic analysis of alcohol vinegar microbiota during an acetification process: a quantitative proteomic approach
10.1016/j.fm.2021.103799 · 2021 · External reference
Metaproteomics – an advantageous option in studies of host-microbiota interaction
10.3390/microorganisms9050980 · 2021 · External reference
10.1038/ismej.2008.108
10.1038/ismej.2008.108 · External reference
Are we really vastly outnumbered? Revisiting the ratio of bacterial to host cells in humans
10.1016/j.cell.2016.01.013 · 2021 · External reference
10.1371/journal.ppat.1009245
10.1371/journal.ppat.1009245 · External reference
Gut microbiome health and dysbiosis: a clinical primer
10.1002/phar.2731 · 2022 · External reference
Oral pathobiont induces systemic inflammation and metabolic changes associated with alteration of gut microbiota
10.1038/srep04828 · 2014 · External reference
Obesity-related gut microbiota aggravates alveolar bone destruction in experimental periodontitis through elevation of uric acid
10.1128/mbio.00771-21 · 2021 · External reference
10.1016/s0140-6736(17)32448-0
10.1016/s0140-6736(17)32448-0 · External reference
Epidemiology of pediatric inflammatory bowel disease: a systematic review of international trends
10.1002/ibd.21349 · 2011 · External reference
Direct health care costs of Crohn’s disease and ulcerative colitis in US children and adults
10.1053/j.gastro.2008.09.012 · 2008 · External reference
Metaproteomics reveals associations between microbiome and intestinal extracellular vesicle proteins in pediatric inflammatory bowel disease
10.1038/s41467-018-05357-4 · 2018 · External reference
10.1007/s00125-012-2672-4
10.1007/s00125-012-2672-4 · External reference
Type 1 diabetes susceptibility alleles are associated with distinct alterations in the gut microbiota
10.1186/s40168-018-0417-4 · 2018 · External reference
10.1126/science.1208344
10.1126/science.1208344 · External reference
10.1016/s0140-6736(16)30507-4
10.1016/s0140-6736(16)30507-4 · External reference
10.2337/dc18-0777
10.2337/dc18-0777 · External reference
Hospital-acquired pneumonia, health care-associated pneumonia, ventilator-associated pneumonia, and ventilator-associated tracheobronchitis: definitions and challenges in trial design
10.1086/653035 · 2010 · External reference
Ventilator-associated pneumonia: diagnosis, treatment, and prevention
10.1128/cmr.00051-05 · 2006 · External reference
Clinical practice guidelines for hospital-acquired pneumonia and ventilator-associated pneumonia in adults
10.1155/2008/593289 · 2008 · External reference
Molecular profiling of innate immune response mechanisms in ventilator-associated Pneumonia
10.1074/mcp.ra120.002207 · 2020 · External reference
Bugs, biofilms, and resistance in cystic fibrosis
10.4187/respcare.09540628 · 2009 · External reference
10.1203/00006450-200003000-00010
10.1203/00006450-200003000-00010 · External reference
Dysbiosis of bifidobacteria and Clostridium cluster XIVa in the cystic fibrosis fecal microbiota
10.1016/j.jcf.2012.10.003 · 2013 · External reference
Escherichia coli dysbiosis correlates with gastrointestinal dysfunction in children with cystic fibrosis
10.1093/cid/cit715 · 2014 · External reference
Faecal proteomics: a tool to investigate dysbiosis and inflammation in patients with cystic fibrosis
10.1016/j.jcf.2015.08.003 · 2016 · External reference
HIV-1 replication and immune dynamics are affected by raltegravir intensification of HAART-suppressed subjects
10.1038/nm.2111 · 2010 · External reference
10.1371/journal.ppat.1003829
10.1371/journal.ppat.1003829 · External reference
10.1016/s2352-3018(15)00045-4
10.1016/s2352-3018(15)00045-4 · External reference
10.1038/mi.2014.107
10.1038/mi.2014.107 · External reference
10.1016/j.ebiom.2016.04.033
10.1016/j.ebiom.2016.04.033 · External reference
Antibiotic prophylaxis for patients with acute leukemia
10.1080/10428190701769673 · 2008 · External reference
10.1126/science.1110591
10.1126/science.1110591 · External reference
10.1126/science.1124234
10.1126/science.1124234 · External reference
Unipept 4.0: functional analysis of metaproteome data
10.1021/acs.jproteome.8b00716 · 2019 · External reference
10.3390/proteomes6010002
10.3390/proteomes6010002 · External reference
Navigating through metaproteomics data: a logbook of database searching
10.1002/pmic.201400560 · 2015 · External reference
10.1016/j.jbiotec.2017.06.1201
10.1016/j.jbiotec.2017.06.1201 · External reference
10.1016/j.csbj.2022.01.018 · Admitted local publication
The impact of sequence database choice on metaproteomic results in gut microbiota studies
10.1186/s40168-016-0196-8 · 2016 · External reference
10.1093/nar/gkx1095
10.1093/nar/gkx1095 · External reference
10.1093/nar/gky1049
10.1093/nar/gky1049 · External reference
10.1038/nature08821
10.1038/nature08821 · External reference
10.1038/nature12506
10.1038/nature12506 · External reference
A framework for human microbiome research
10.1038/nature11209 · 2012 · External reference
10.1038/nature11450
10.1038/nature11450 · External reference
10.1038/nbt.2942
10.1038/nbt.2942 · External reference
10.1093/dnares/dsw002
10.1093/dnares/dsw002 · External reference
10.1038/s41587-018-0008-8
10.1038/s41587-018-0008-8 · External reference
10.1038/s41587-018-0009-7
10.1038/s41587-018-0009-7 · External reference
10.1038/s41587-020-0603-3
10.1038/s41587-020-0603-3 · External reference
10.1093/nar/gkv1070
10.1093/nar/gkv1070 · External reference
10.1007/978-1-60761-444-9_5
10.1007/978-1-60761-444-9_5 · External reference
DecoyPyrat: fast non-redundant hybrid decoy sequence generation for large scale proteomics
10.4172/jpb.1000404 · 2016 · External reference
10.1002/pmic.201200352
10.1002/pmic.201200352 · External reference
Benefits of iterative searches of large databases to interpret large human gut metaproteomic data sets
10.1021/acs.jproteome.0c00669 · 2021 · External reference
A sectioning and database enrichment approach for improved peptide spectrum matching in large, genome-guided protein sequence databases
10.1021/acs.jproteome.0c00260 · 2020 · External reference
10.1186/s40168-016-0176-z
10.1186/s40168-016-0176-z · External reference
10.1021/acs.jproteome.7b00894
10.1021/acs.jproteome.7b00894 · External reference
10.1038/nmeth1113
10.1038/nmeth1113 · External reference
10.1021/ac025747h
10.1021/ac025747h · External reference
TIDD: tool-independent and data-dependent machine learning for peptide identification
10.1186/s12859-022-04640-y · 2022 · External reference
Beyond target-decoy competition: stable validation of peptide and protein identifications in mass spectrometry-based discovery proteomics
10.1021/acs.analchem.0c00328 · 2020 · External reference
10.4161/gmic.2.1.14651 · 2011 · Admitted local publication
Statistical calibration of the SEQUEST XCorr function
10.1021/pr8011107 · 2009 · External reference
Controlling the false discovery rate: a practical and powerful approach to multiple testing
10.1111/j.2517-6161.1995.tb02031.x · 1995 · External reference
The microbiome as a human organ
10.1111/j.1469-0691.2012.03916.x · 2012 · External reference
10.1074/mcp.o111.016717
10.1074/mcp.o111.016717 · External reference
10.1074/mcp.ra117.000314
10.1074/mcp.ra117.000314 · External reference
Metaproteomics characterizes human gut microbiome function in colorectal cancer
10.1038/s41522-020-0123-4 · 2020 · External reference
Data-independent acquisition mass spectrometry in metaproteomics of gut microbiota-implementation and computational analysis
10.1021/acs.jproteome.9b00606 · 2020 · External reference
Introducing untargeted data-independent acquisition for metaproteomics of complex microbial samples
10.1038/s43705-022-00137-0 · 2022 · External reference
10.1016/j.csbj.2022.03.008 · Admitted local publication
10.1021/acs.jproteome.2c00334
10.1021/acs.jproteome.2c00334 · External reference
The current state-of-the-art identification of unknown proteins using mass spectrometry exemplified on de novo sequencing of a venom protease from Bothrops moojeni
10.3390/molecules27154976 · 2022 · External reference
