Platforms and Pipelines for Proteomics Data Analysis and Management (Q31148953)

29 June 2017

Platforms and Pipelines for Proteomics Data Analysis and Management (English)

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29 June 2017

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Marius Cosmin Codrea

1

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29 June 2017

Sven Nahnsen

series ordinal

2

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29 June 2017

language of work or name

English

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publication date

1 January 2016

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Advances in Experimental Medicine and Biology

29 June 2017

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29 June 2017

919

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29 June 2017

203-215

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Characterization of native protein complexes and protein isoform variation using size-fractionation-based quantitative proteomics

29 June 2017

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-41448-5_9

A draft map of the human proteome

21 January 2018

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https://api.crossref.org/works/10.1007%2F978-3-319-41448-5_9

Options and considerations when selecting a quantitative proteomics strategy

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-41448-5_9

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-41448-5_9

An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-41448-5_9

Probability-based protein identification by searching sequence databases using mass spectrometry data

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-41448-5_9

Open mass spectrometry search algorithm

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-41448-5_9

Andromeda: a peptide search engine integrated into the MaxQuant environment

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-41448-5_9

A face in the crowd: recognizing peptides through database search

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-41448-5_9

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-41448-5_9

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-41448-5_9

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-41448-5_9

A guided tour of the Trans-Proteomic Pipeline

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-41448-5_9

OpenMS - an open-source software framework for mass spectrometry

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-41448-5_9

msCompare: a framework for quantitative analysis of label-free LC-MS data for comparative candidate biomarker studies

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-41448-5_9

Editorial: from data to results

21 January 2018

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https://api.crossref.org/works/10.1007%2F978-3-319-41448-5_9

Open source libraries and frameworks for mass spectrometry based proteomics: a developer's perspective

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-41448-5_9

The mzTab data exchange format: communicating mass-spectrometry-based proteomics and metabolomics experimental results to a wider audience

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-41448-5_9

File formats commonly used in mass spectrometry proteomics

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-41448-5_9

A tutorial for software development in quantitative proteomics using PSI standard formats

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-41448-5_9

mz5: space- and time-efficient storage of mass spectrometry data sets

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-41448-5_9

ProteoWizard: open source software for rapid proteomics tools development

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-41448-5_9

A cross-platform toolkit for mass spectrometry and proteomics

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-41448-5_9

A dual pressure linear ion trap Orbitrap instrument with very high sequencing speed.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-41448-5_9

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-41448-5_9

Tools for label-free peptide quantification

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-41448-5_9

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-41448-5_9

A statistical model for identifying proteins by tandem mass spectrometry

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-41448-5_9

Protein identification false discovery rates for very large proteomics data sets generated by tandem mass spectrometry

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-41448-5_9

Bayesian proteoform modeling improves protein quantification of global proteomic measurements.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-41448-5_9

Quantitative analysis of complex protein mixtures using isotope-coded affinity tags

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-41448-5_9

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-41448-5_9

Quantitative mass spectrometry in proteomics: a critical review

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-41448-5_9

IsoQuant: a software tool for stable isotope labeling by amino acids in cell culture-based mass spectrometry quantitation.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-41448-5_9

IQuant: an automated pipeline for quantitative proteomics based upon isobaric tags.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-41448-5_9

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-41448-5_9

Role of spectral counting in quantitative proteomics.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-41448-5_9

Hyperplexing: a method for higher-order multiplexed quantitative proteomics provides a map of the dynamic response to rapamycin in yeast

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-41448-5_9

A geometric approach for the alignment of liquid chromatography-mass spectrometry data

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-41448-5_9

TOPP--the OpenMS proteomics pipeline

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-41448-5_9

Critical assessment of alignment procedures for LC-MS proteomics and metabolomics measurements

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-41448-5_9

qcML: an exchange format for quality control metrics from mass spectrometry experiments

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-41448-5_9

Software pipeline and data analysis for MS/MS proteomics: the trans-proteomic pipeline

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-41448-5_9

iProphet: multi-level integrative analysis of shotgun proteomic data improves peptide and protein identification rates and error estimates

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-41448-5_9

Comet: an open-source MS/MS sequence database search tool

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-41448-5_9

TANDEM: matching proteins with tandem mass spectra

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-41448-5_9

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-41448-5_9

InsPecT: identification of posttranslationally modified peptides from tandem mass spectra

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-41448-5_9

MyriMatch: highly accurate tandem mass spectral peptide identification by multivariate hypergeometric analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-41448-5_9

Building consensus spectral libraries for peptide identification in proteomics

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-41448-5_9

Automated statistical analysis of protein abundance ratios from data generated by stable-isotope dilution and tandem mass spectrometry

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-41448-5_9

Quantitative profiling of differentiation-induced microsomal proteins using isotope-coded affinity tags and mass spectrometry

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-41448-5_9

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-41448-5_9

TOPPAS: a graphical workflow editor for the analysis of high-throughput proteomics data

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-41448-5_9

CPFP: a central proteomics facilities pipeline

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-41448-5_9

DTASelect and Contrast: tools for assembling and comparing protein identifications from shotgun proteomics

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-41448-5_9

Validation of tandem mass spectrometry database search results using DTASelect

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-41448-5_9

MS1, MS2, and SQT-three unified, compact, and easily parsed file formats for the storage of shotgun proteomic spectra and identifications.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-41448-5_9

A guide to the Proteomics Identifications Database proteomics data repository

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-41448-5_9

PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-41448-5_9

Scaffold: a bioinformatic tool for validating MS/MS-based proteomic studies

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-41448-5_9

A quantitative analysis software tool for mass spectrometry-based proteomics

31 March 2020

1 reference

https://api.crossref.org/works/10.1007%2F978-3-319-41448-5_9

10.1007/978-3-319-41448-5_9

31 March 2020

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