Spiked proteomic standard dataset for testing label-free quantitative software and statistical methods. (Q36446071)

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7 March 2020

title

Spiked proteomic standard dataset for testing label-free quantitative software and statistical methods (English)

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4

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Christine Carapito

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Myriam Ferro

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Yohann Couté

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Anne Gonzalez de Peredo

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Odile Burlet-Schiltz

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David Bouyssié

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Emmanuelle Mouton-Barbosa

7 March 2020

5

object named as

Emmanuelle Mouton-Barbosa

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Karima Chaoui

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3

Marlène Marcellin

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7 March 2020

author name string

Claire Ramus

1

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Agnès Hovasse

2

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Sebastian Vaca

7

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Christophe Bruley

10

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Sarah Cianférani

12

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7 March 2020

Alain Van Dorssaeler

14

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Christine Schaeffer

16

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Jérôme Garin

11

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publication date

17 December 2015

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7 March 2020

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volume

6

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7 March 2020

page(s)

286-294

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Benchmarking quantitative label-free LC-MS data processing workflows using a complex spiked proteomic standard dataset.

7 March 2020

cites work

1 reference

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Accurate proteome-wide label-free quantification by delayed normalization and maximal peptide ratio extraction, termed MaxLFQ.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4706616

Label-free quantification and shotgun analysis of complex proteomes by one-dimensional SDS-PAGE/NanoLC-MS: evaluation for the large scale analysis of inflammatory human endothelial cells

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4706616

Platform-independent and label-free quantitation of proteomic data using MS1 extracted ion chromatograms in skyline: application to protein acetylation and phosphorylation

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4706616

Andromeda: a peptide search engine integrated into the MaxQuant environment

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4706616

Skyline: an open source document editor for creating and analyzing targeted proteomics experiments

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4706616

In-depth exploration of cerebrospinal fluid by combining peptide ligand library treatment and label-free protein quantification

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4706616

On the beta-binomial model for analysis of spectral count data in label-free tandem mass spectrometry-based proteomics

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4706616

A toolbox for validation of mass spectrometry peptides identification and generation of database: IRMa

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4706616

A practical guide to the MaxQuant computational platform for SILAC-based quantitative proteomics

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4706616

MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4706616

Proteomic parsimony through bipartite graph analysis improves accuracy and transparency

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4706616

Mascot file parsing and quantification (MFPaQ), a new software to parse, validate, and quantify proteomics data generated by ICAT and SILAC mass spectrometric analyses: application to the proteomics study of membrane proteins from primary human [...]

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4706616

A refined method to calculate false discovery rates for peptide identification using decoy databases.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4706616

10.1016/J.DIB.2015.11.063

21 September 2018

Identifiers

DOI

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7 March 2020

1 reference

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7 March 2020

PubMed publication ID

26862574

1 reference

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