(Q55402062)

6 July 2018

title

Benchmarking common quantification strategies for large-scale phosphoproteomics. (English)

1 reference

6 July 2018

author

Christian D. Kelstrup

5

1 reference

6 July 2018

Jesper V. Olsen

6

1 reference

6 July 2018

Alexander Hogrebe

object named as

Alexander Hogrebe

1

0 references

Brian T Weinert

object named as

Brian T Weinert

4

0 references

author name string

Louise von Stechow

2

1 reference

6 July 2018

Dorte B Bekker-Jensen

3

1 reference

6 July 2018

language of work or name

English

0 references

publication date

13 March 2018

1 reference

6 July 2018

published in

Nature Communications

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6 July 2018

volume

9

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6 July 2018

issue

1

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6 July 2018

page(s)

1045

1 reference

6 July 2018

Creative Commons Attribution 4.0 International

copyright license

start time

13 March 2018

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

describes a project that uses

1 reference

10 June 2022

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pmc&rettype=xml&id=5849679

exact match

https://scigraph.springernature.com/pub.10.1038/s41467-018-03309-6

0 references

cites work

An Optimized Shotgun Strategy for the Rapid Generation of Comprehensive Human Proteomes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5849679

Deep Coverage of Global Protein Expression and Phosphorylation in Breast Tumor Cell Lines Using TMT 10-plex Isobaric Labeling

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5849679

On the Statistical Significance of Compressed Ratios in Isobaric Labeling: A Cross-Platform Comparison

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5849679

The Perseus computational platform for comprehensive analysis of (prote)omics data

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5849679

Uses and misuses of the fudge factor in quantitative discovery proteomics.

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5849679

Proteogenomics connects somatic mutations to signalling in breast cancer

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5849679

2016 update of the PRIDE database and its related tools

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5849679

Large-scale determination of absolute phosphorylation stoichiometries in human cells by motif-targeting quantitative proteomics

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5849679

Evaluating multiplexed quantitative phosphopeptide analysis on a hybrid quadrupole mass filter/linear ion trap/orbitrap mass spectrometer

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5849679

Off-line high-pH reversed-phase fractionation for in-depth phosphoproteomics

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5849679

Comparing SILAC- and stable isotope dimethyl-labeling approaches for quantitative proteomics

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5849679

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

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5849679

MultiNotch MS3 enables accurate, sensitive, and multiplexed detection of differential expression across cancer cell line proteomes.

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5849679

ProteomeXchange provides globally coordinated proteomics data submission and dissemination

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5849679

Ion coalescence of neutron encoded TMT 10-plex reporter ions.

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5849679

Novel parallelized quadrupole/linear ion trap/Orbitrap tribrid mass spectrometer improving proteome coverage and peptide identification rates.

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5849679

In Vivo Phosphoproteomics Analysis Reveals the Cardiac Targets of -Adrenergic Receptor Signaling

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5849679

Accurate multiplexed proteomics at the MS2 level using the complement reporter ion cluster.

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5849679

Quantitative maps of protein phosphorylation sites across 14 different rat organs and tissues

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5849679

Proteomic investigations reveal a role for RNA processing factor THRAP3 in the DNA damage response

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5849679

iTRAQ labeling is superior to mTRAQ for quantitative global proteomics and phosphoproteomics

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5849679

Gas-phase purification enables accurate, multiplexed proteome quantification with isobaric tagging

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5849679

MS3 eliminates ratio distortion in isobaric multiplexed quantitative proteomics

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5849679

A large-scale method to measure absolute protein phosphorylation stoichiometries

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5849679

Mass spectrometry-based proteomics using Q Exactive, a high-performance benchtop quadrupole Orbitrap mass spectrometer.

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5849679

A tissue-specific atlas of mouse protein phosphorylation and expression

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5849679

Peptide labeling with isobaric tags yields higher identification rates using iTRAQ 4-plex compared to TMT 6-plex and iTRAQ 8-plex on LTQ Orbitrap

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5849679

Addressing accuracy and precision issues in iTRAQ quantitation

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5849679

Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5849679

iTRAQ underestimation in simple and complex mixtures: "the good, the bad and the ugly".

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5849679

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

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5849679

The SCX/IMAC enrichment approach for global phosphorylation analysis by mass spectrometry

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5849679

Protocol for micro-purification, enrichment, pre-fractionation and storage of peptides for proteomics using StageTips

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5849679

ATM and ATR substrate analysis reveals extensive protein networks responsive to DNA damage

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5849679

Global, in vivo, and site-specific phosphorylation dynamics in signaling networks

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5849679

Highly selective enrichment of phosphorylated peptides from peptide mixtures using titanium dioxide microcolumns.

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5849679

Tandem Mass Tags: A Novel Quantification Strategy for Comparative Analysis of Complex Protein Mixtures by MS/MS

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5849679

Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5849679

Significance analysis of microarrays applied to the ionizing radiation response

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5849679

Performance Evaluation of the Q Exactive HF-X for Shotgun Proteomics

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5849679

Improvement of Quantitative Measurements in Multiplex Proteomics Using High-Field Asymmetric Waveform Spectrometry.

12 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5849679

Simple and Reproducible Sample Preparation for Single-Shot Phosphoproteomics with High Sensitivity.

12 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5849679

Rapid and deep proteomes by faster sequencing on a benchtop quadrupole ultra-high-field Orbitrap mass spectrometer

12 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5849679

Measuring and managing ratio compression for accurate iTRAQ/TMT quantification.

12 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5849679

Benchmarking stable isotope labeling based quantitative proteomics

12 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5849679

Optimized fast and sensitive acquisition methods for shotgun proteomics on a quadrupole orbitrap mass spectrometer.

12 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5849679

Systematic comparison of label-free, metabolic labeling, and isobaric chemical labeling for quantitative proteomics on LTQ Orbitrap Velos.

12 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5849679

High-performance hybrid Orbitrap mass spectrometers for quantitative proteome analysis: Observations and implications

12 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5849679

Improved visualization of protein consensus sequences by iceLogo

30 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5849679

Protein labeling by iTRAQ: A new tool for quantitative mass spectrometry in proteome research

30 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5849679

Isolation of phosphoproteins by immobilized metal (Fe3+) affinity chromatography

30 November 2018

1 reference

Crossref

https://api.crossref.org/works/10.1038%2FS41467-018-03309-6

inferred from DOI database lookup

7 January 2021

based on heuristic

SILAC yeast: from labeling to comprehensive proteome quantification

1 reference

Crossref

https://api.crossref.org/works/10.1038%2FS41467-018-03309-6

inferred from DOI database lookup

7 January 2021

based on heuristic

Identifiers

DOI

10.1038/S41467-018-03309-6

1 reference

6 July 2018

Dimensions Publication ID

ADS bibcode

2018NatCo...9.1045H

0 references

0 references

1 reference

6 July 2018

PubMed ID

29535314

1 reference

6 July 2018