DeMix-Q: Quantification-Centered Data Processing Workflow (Q30739756)

16 September 2017

DeMix-Q: Quantification-Centered Data Processing Workflow (English)

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16 September 2017

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Roman A Zubarev

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Bo Zhang

object named as

Bo Zhang

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1

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Lukas Käll

object named as

Lukas Käll

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2

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publication date

4 January 2016

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Molecular & Cellular Proteomics

16 September 2017

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16 September 2017

15

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16 September 2017

4

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16 September 2017

1467-1478

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MaRaCluster: A Fragment Rarity Metric for Clustering Fragment Spectra in Shotgun Proteomics

16 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4824868

Solution to Statistical Challenges in Proteomics Is More Statistics, Not Less

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4824868

Peptide-Centric Proteome Analysis: An Alternative Strategy for the Analysis of Tandem Mass Spectrometry Data

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4824868

Review, evaluation, and discussion of the challenges of missing value imputation for mass spectrometry-based label-free global proteomics

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4824868

Reproducible and consistent quantification of the Saccharomyces cerevisiae proteome by SWATH-mass spectrometry

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4824868

MS-GF+ makes progress towards a universal database search tool for proteomics

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4824868

DeMix workflow for efficient identification of cofragmented peptides in high resolution data-dependent tandem mass spectrometry

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4824868

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4824868

Intelligent data acquisition blends targeted and discovery methods

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4824868

Improved intensity-based label-free quantification via proximity-based intensity normalization (PIN).

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4824868

Improved normalization of systematic biases affecting ion current measurements in label-free proteomics data

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4824868

LC-MS alignment in theory and practice: a comprehensive algorithmic review

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4824868

Mass fingerprinting of complex mixtures: protein inference from high-resolution peptide masses and predicted retention times

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4824868

Rapid and deep human proteome analysis by single-dimension shotgun proteomics.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4824868

Maximizing peptide identification events in proteomic workflows using data-dependent acquisition (DDA).

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4824868

Multiplexed MS/MS for improved data-independent acquisition

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4824868

In silico instrumental response correction improves precision of label-free proteomics and accuracy of proteomics-based predictive models.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4824868

An automated pipeline for high-throughput label-free quantitative proteomics

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4824868

Segmentation of precursor mass range using "tiling" approach increases peptide identifications for MS1-based label-free quantification

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4824868

Statistical protein quantification and significance analysis in label-free LC-MS experiments with complex designs

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4824868

Parallel reaction monitoring for high resolution and high mass accuracy quantitative, targeted proteomics

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4824868

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4824868

Comparative proteomic analysis of eleven common cell lines reveals ubiquitous but varying expression of most proteins

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4824868

Targeted data extraction of the MS/MS spectra generated by data-independent acquisition: a new concept for consistent and accurate proteome analysis

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4824868

A framework for intelligent data acquisition and real-time database searching for shotgun proteomics

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4824868

Enhanced information output from shotgun proteomics data by protein quantification and peptide quality control (PQPQ).

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4824868

More than 100,000 detectable peptide species elute in single shotgun proteomics runs but the majority is inaccessible to data-dependent LC-MS/MS.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4824868

COMPASS: a suite of pre- and post-search proteomics software tools for OMSSA

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4824868

Less label, more free: approaches in label-free quantitative mass spectrometry.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4824868

Options and considerations when selecting a quantitative proteomics strategy

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4824868

Repeatability and reproducibility in proteomic identifications by liquid chromatography-tandem mass spectrometry

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4824868

Protein quantification across hundreds of experimental conditions.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4824868

IDPicker 2.0: Improved protein assembly with high discrimination peptide identification filtering

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4824868

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4824868

Comparative LC-MS: a landscape of peaks and valleys

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4824868

Label-free comparative analysis of proteomics mixtures using chromatographic alignment of high-resolution muLC-MS data

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4824868

An assessment of software solutions for the analysis of mass spectrometry based quantitative proteomics data

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4824868

Analysis and validation of proteomic data generated by tandem mass spectrometry

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4824868

How do shotgun proteomics algorithms identify proteins?

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4824868

TOPP--the OpenMS proteomics pipeline

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4824868

PEPPeR, a platform for experimental proteomic pattern recognition.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4824868

Absolute quantification of proteins by LCMSE: a virtue of parallel MS acquisition

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4824868

Proteomic analyses using an accurate mass and time tag strategy

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4824868

Computational strategies for analyzing data in gene expression microarray experiments

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4824868

The use of accurate mass tags for high-throughput microbial proteomics

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4824868

Efficient error correction for next-generation sequencing of viral amplicons

20 June 2018

1 reference

https://api.crossref.org/works/10.1074%2FMCP.O115.055475

Differential mass spectrometry: a label-free LC-MS method for finding significant differences in complex peptide and protein mixtures.

21 January 2018

1 reference

https://api.crossref.org/works/10.1074%2FMCP.O115.055475

An integrated mass spectrometric and computational framework for the analysis of protein interaction networks.

21 January 2018

1 reference

https://api.crossref.org/works/10.1074%2FMCP.O115.055475

Semi-supervised learning for peptide identification from shotgun proteomics datasets.

21 January 2018

1 reference

https://api.crossref.org/works/10.1074%2FMCP.O115.055475

21 January 2018

Identifiers

DOI

10.1074/MCP.O115.055475

1 reference

16 September 2017

1 reference

PMC publication ID

4824868

16 September 2017

PubMed publication ID

26729709

1 reference

PMC publication ID

4824868