15. Since the de novo search results will only be used to establish
which species proteomes will be included in the targeted
search, strict search rules will not affect the final result outcome. In addition, it is recommended to set both the fragment
and ion tolerance narrow, highly improving the number of
identified peptides.
16. For FDR control, a reversed protein sequence can be created
with ProteoClade by changing the reverse parameter to True
when executing the pcdb command. The annotation steps can
then be repeated against this database.
Acknowledgments
This work was supported by the European Research Council ERC
(694181), National Institute of Allergy and Infectious Diseases
(U01AI095473, the content is solely the responsibility of the authors
and does not necessarily represent the official views of the NIH), The
Knut and Alice Wallenberg Foundation (2017.0028), Swedish
Research Council (2017-00958), The Swedish Cancer Foundation (CAN 2017/360), IngaBritt and Arne Lundberg Foundation,
Sahlgren’s University Hospital (ALFGBG-440741, The ALF agreement 236501), Bill and Melinda Gates Foundation
(OPP1202459) and Wilhelm and Martina Lundgren’s Foundation.
SVDP is supported by the SSMF foundation (P17-0060).
References
1. Johansson MEV, Ambort D, Pelaseyed T et al
(2011) Composition and functional role of the
mucus layers in the intestine. Cell Mol Life Sci
68:3635–3641.
https://doi.org/10.1007/
s00018-011-0822-3
2. Wu H, Tremaroli V, B€ ackhed F (2015) Linking
microbiota to human diseases: a systems biology perspective. Trends Endocrinol Metab
26:758–770.
https://doi.org/10.1016/j.
tem.2015.09.011
3. Heintz-Buschart A, Wilmes P (2018) Human
gut microbiome: function matters. Trends
Microbiol 26:563–574. https://doi.org/10.
1016/j.tim.2017.11.002
4. Xiong W, Giannone RJ, Morowitz MJ et al
(2015) Development of an enhanced metaproteomic approach for deepening the microbiome characterization of the human infant
gut. J Proteome Res 14:133–141. https://
doi.org/10.1021/pr500936p
5. Tanca A, Palomba A, Pisanu S et al (2015)
Enrichment or depletion? The impact of stool
pretreatment
on
metaproteomic
characterization of the human gut microbiota.
Proteomics 15:3474–3485. https://doi.org/
10.1002/pmic.201400573
6. Zhang X, Deeke SA, Ning Z et al (2018) Metaproteomics reveals associations between microbiome and intestinal extracellular vesicle
proteins in pediatric inflammatory bowel disease. Nat Commun 9:1–14. https://doi.org/
10.1038/s41467-018-05357-4
7. Li X, LeBlanc J, Truong A et al (2011) A
metaproteomic approach to study humanmicrobial ecosystems at the mucosal luminal
interface. PLoS One 6:e26542. https://doi.
org/10.1371/journal.pone.0026542
8. Heyer R, Schallert K, Zoun R et al (2017)
Challenges and perspectives of metaproteomic
data analysis. J Biotechnol 261:24–36. https://
doi.org/10.1016/j.jbiotec.2017.06.1201
9. Steen H, Mann M (2004) The ABC’s (and
XYZ’s) of peptide sequencing. Nat Rev Mol
Cell Biol 5:699–711. https://doi.org/10.
1038/nrm1468
178
Sjoerd van der Post and Liisa Arike
which species proteomes will be included in the targeted
search, strict search rules will not affect the final result outcome. In addition, it is recommended to set both the fragment
and ion tolerance narrow, highly improving the number of
identified peptides.
16. For FDR control, a reversed protein sequence can be created
with ProteoClade by changing the reverse parameter to True
when executing the pcdb command. The annotation steps can
then be repeated against this database.
Acknowledgments
This work was supported by the European Research Council ERC
(694181), National Institute of Allergy and Infectious Diseases
(U01AI095473, the content is solely the responsibility of the authors
and does not necessarily represent the official views of the NIH), The
Knut and Alice Wallenberg Foundation (2017.0028), Swedish
Research Council (2017-00958), The Swedish Cancer Foundation (CAN 2017/360), IngaBritt and Arne Lundberg Foundation,
Sahlgren’s University Hospital (ALFGBG-440741, The ALF agreement 236501), Bill and Melinda Gates Foundation
(OPP1202459) and Wilhelm and Martina Lundgren’s Foundation.
SVDP is supported by the SSMF foundation (P17-0060).
References
1. Johansson MEV, Ambort D, Pelaseyed T et al
(2011) Composition and functional role of the
mucus layers in the intestine. Cell Mol Life Sci
68:3635–3641.
https://doi.org/10.1007/
s00018-011-0822-3
2. Wu H, Tremaroli V, B€ ackhed F (2015) Linking
microbiota to human diseases: a systems biology perspective. Trends Endocrinol Metab
26:758–770.
https://doi.org/10.1016/j.
tem.2015.09.011
3. Heintz-Buschart A, Wilmes P (2018) Human
gut microbiome: function matters. Trends
Microbiol 26:563–574. https://doi.org/10.
1016/j.tim.2017.11.002
4. Xiong W, Giannone RJ, Morowitz MJ et al
(2015) Development of an enhanced metaproteomic approach for deepening the microbiome characterization of the human infant
gut. J Proteome Res 14:133–141. https://
doi.org/10.1021/pr500936p
5. Tanca A, Palomba A, Pisanu S et al (2015)
Enrichment or depletion? The impact of stool
pretreatment
on
metaproteomic
characterization of the human gut microbiota.
Proteomics 15:3474–3485. https://doi.org/
10.1002/pmic.201400573
6. Zhang X, Deeke SA, Ning Z et al (2018) Metaproteomics reveals associations between microbiome and intestinal extracellular vesicle
proteins in pediatric inflammatory bowel disease. Nat Commun 9:1–14. https://doi.org/
10.1038/s41467-018-05357-4
7. Li X, LeBlanc J, Truong A et al (2011) A
metaproteomic approach to study humanmicrobial ecosystems at the mucosal luminal
interface. PLoS One 6:e26542. https://doi.
org/10.1371/journal.pone.0026542
8. Heyer R, Schallert K, Zoun R et al (2017)
Challenges and perspectives of metaproteomic
data analysis. J Biotechnol 261:24–36. https://
doi.org/10.1016/j.jbiotec.2017.06.1201
9. Steen H, Mann M (2004) The ABC’s (and
XYZ’s) of peptide sequencing. Nat Rev Mol
Cell Biol 5:699–711. https://doi.org/10.
1038/nrm1468
178
Sjoerd van der Post and Liisa Arike