Evaluating the impact of different sequence databases on metaproteome analysis: insights from a lab-assembled microbial mixture (Q35070680)

6 August 2017

Evaluating the impact of different sequence databases on metaproteome analysis: insights from a lab-assembled microbial mixture (English)

1 reference

6 August 2017

Alessandro Tanca

1

0 references

Massimo Deligios

object named as

Massimo Deligios

3

0 references

Maria Filippa Addis

object named as

Maria Filippa Addis

8

0 references

author name string

Antonio Palomba

2

1 reference

6 August 2017

Tiziana Cubeddu

4

1 reference

6 August 2017

Cristina Fraumene

5

1 reference

6 August 2017

Grazia Biosa

6

1 reference

6 August 2017

Daniela Pagnozzi

7

1 reference

6 August 2017

Sergio Uzzau

9

1 reference

6 August 2017

language of work or name

English

0 references

publication date

9 December 2013

1 reference

6 August 2017

1 reference

6 August 2017

8

1 reference

6 August 2017

12

1 reference

6 August 2017

e82981

1 reference

Creative Commons Attribution 3.0 Unported

6 August 2017

start time

9 December 2013

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

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cites work

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8 July 2018

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Bioinformatic progress and applications in metaproteogenomics for bridging the gap between genomic sequences and metabolic functions in microbial communities

8 July 2018

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Going local: technologies for exploring bacterial microenvironments

8 July 2018

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A two-step database search method improves sensitivity in peptide sequence matches for metaproteomics and proteogenomics studies.

8 July 2018

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Waiting for the human intestinal Eukaryotome

8 July 2018

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Searching for a needle in a stack of needles: challenges in metaproteomics data analysis

8 July 2018

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Integrated metagenomics/metaproteomics reveals human host-microbiota signatures of Crohn's disease

8 July 2018

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Unipept: tryptic peptide-based biodiversity analysis of metaproteome samples.

8 July 2018

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Current algorithmic solutions for peptide-based proteomics data generation and identification

8 July 2018

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Application of 2D-DIGE to formalin-fixed diseased tissue samples from hospital repositories: results from four case studies

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3857319

Microbial culturomics: paradigm shift in the human gut microbiome study

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3857319

The function of our microbiota: who is out there and what do they do?

8 July 2018

1 reference

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Inference and validation of protein identifications

8 July 2018

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Metagenomics: microbial diversity through a scratched lens

8 July 2018

1 reference

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Interspecific interactions in mixed microbial cultures in a biodegradation perspective

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3857319

Structure, function and diversity of the healthy human microbiome

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3857319

Interactions between commensal fungi and the C-type lectin receptor Dectin-1 influence colitis

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3857319

Microbial metaproteomics: identifying the repertoire of proteins that microorganisms use to compete and cooperate in complex environmental communities.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3857319

Deep metaproteomic analysis of human salivary supernatant.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3857319

Modeling microbial communities: current, developing, and future technologies for predicting microbial community interaction

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3857319

The human microbiome: at the interface of health and disease

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3857319

Protein inference: a review.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3857319

Exploring mixed microbial community functioning: recent advances in metaproteomics.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3857319

Microbial communities involved in enhanced biological phosphorus removal from wastewater--a model system in environmental biotechnology

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3857319

Strategies for metagenomic-guided whole-community proteomics of complex microbial environments

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3857319

Reorganizing the protein space at the Universal Protein Resource (UniProt)

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3857319

Generic comparison of protein inference engines

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3857319

Our microbial selves: what ecology can teach us

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3857319

Integrative analysis of environmental sequences using MEGAN4

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3857319

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3857319

An iterative workflow for mining the human intestinal metaproteome

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3857319

Direct cellular lysis/protein extraction protocol for soil metaproteomics

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3857319

A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3857319

Systems approaches to microbial communities and their functioning.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3857319

A metaproteomic analysis of the human salivary microbiota by three-dimensional peptide fractionation and tandem mass spectrometry.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3857319

Prodigal: prokaryotic gene recognition and translation initiation site identification

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3857319

Cross species proteomics.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3857319

De novo sequencing of peptides by MS/MS.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3857319

Community proteogenomics reveals insights into the physiology of phyllosphere bacteria

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3857319

Improvements to the percolator algorithm for Peptide identification from shotgun proteomics data sets

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3857319

Universal sample preparation method for proteome analysis

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3857319

Systems biology: Functional analysis of natural microbial consortia using community proteomics

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3857319

Metagenomics approaches in systems microbiology

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3857319

Velvet: algorithms for de novo short read assembly using de Bruijn graphs

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3857319

Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3857319

MEGAN analysis of metagenomic data

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3857319

Metaproteomics: studying functional gene expression in microbial ecosystems

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3857319

Interpretation of shotgun proteomic data: the protein inference problem

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3857319

Metagenomics: genomic analysis of microbial communities

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3857319

Rapid isolation of yeast genomic DNA: Bust n' Grab

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3857319

Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3857319

Charting the proteomes of organisms with unsequenced genomes by MALDI-quadrupole time-of-flight mass spectrometry and BLAST homology searching

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3857319

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3857319

Comparison of detergent-based sample preparation workflows for LTQ-Orbitrap analysis of the Escherichia coli proteome.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3857319

Microbial interactions during residual oil and n-fatty acid metabolism by a methanogenic consortium.

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3857319

Database resources of the National Center for Biotechnology Information

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3857319

Coupling a detergent lysis/cleanup methodology with intact protein fractionation for enhanced proteome characterization.

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3857319

Addressing statistical biases in nucleotide-derived protein databases for proteogenomic search strategies

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3857319

Introduction to the analysis of environmental sequences: metagenomics with MEGAN.

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3857319

Proteogenomic analysis of Candida glabrata using high resolution mass spectrometry.

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3857319

Analysis of the resolution limitations of peptide identification algorithms.

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3857319

A protein processing filter method for bacterial identification by mass spectrometry-based proteomics

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3857319

Comparative metaproteomics reveals ocean-scale shifts in microbial nutrient utilization and energy transduction

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3857319

Proteomics-inferred genome typing (PIGT) demonstrates inter-population recombination as a strategy for environmental adaptation.

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3857319

Microbiology: metagenomics

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3857319

Performance evaluation of existing de novo sequencing algorithms.

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3857319

Community proteomics of a natural microbial biofilm

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3857319

Shotgun metaproteomics of the human distal gut microbiota

27 September 2018

1 reference

Crossref

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0082981

Peptide identification quality control

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0082981

Quality assessments of peptide-spectrum matches in shotgun proteomics

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0082981

21 January 2018

Tackling the microbiome.

1 reference

12 December 2020

Mucosal immunology: Don't forget our fungal friends

1 reference

12 December 2020

Microbiota from the distal guts of lean and obese adolescents exhibit partial functional redundancy besides clear differences in community structure

1 reference

12 December 2020

Estimating the confidence of peptide identifications without decoy databases

1 reference

12 December 2020

10.1371/JOURNAL.PONE.0082981

Identifiers

DOI

1 reference

6 August 2017

0 references

1 reference

6 August 2017

1 reference