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List of works by Eric W Deutsch

A Bovine PeptideAtlas of milk and mammary gland proteomes ⬇️

scientific article published on September 1, 2012

A Candida albicans PeptideAtlas

scientific article published on 26 June 2013

A Comprehensive Evaluation of Consensus Spectrum Generation Methods in Proteomics

publication published on 13 May 2022

A HUPO test sample study reveals common problems in mass spectrometry-based proteomics

scientific article published on June 2009

A Tandem Mass Spectrometry Sequence Database Search Method for Identification of O-Fucosylated Proteins by Mass Spectrometry

article

A Technique for Narrowband Time Series Photometry: The X‐Ray Star V2116 Ophiuchi

scholarly article

A chromosome-centric human proteome project (C-HPP) to characterize the sets of proteins encoded in chromosome 17.

scientific article

A common open representation of mass spectrometry data and its application to proteomics research

scientific article

A complete mass-spectrometric map of the yeast proteome applied to quantitative trait analysis

scientific article

A comprehensive Candida albicans PeptideAtlas build enables deep proteome coverage

scientific article

A cross-platform toolkit for mass spectrometry and proteomics

scientific article

A database of mass spectrometric assays for the yeast proteome

scientific article

A dataset of human liver proteins identified by protein profiling via isotope-coded affinity tag (ICAT) and tandem mass spectrometry

scientific article published on 21 July 2004

A global Staphylococcus aureus proteome resource applied to the in vivo characterization of host-pathogen interactions

scientific article published on 8 September 2017

A guided tour of the Trans-Proteomic Pipeline

scientific article

A high-confidence human plasma proteome reference set with estimated concentrations in PeptideAtlas

scientific article

A high-quality catalog of the Drosophila melanogaster proteome

scientific article

A high-stringency blueprint of the human proteome

scientific article published on 16 October 2020

A honey bee (Apis mellifera L.) PeptideAtlas crossing castes and tissues ⬇️

scientific article published on June 3, 2011

A mouse plasma peptide atlas as a resource for disease proteomics

scientific article published on 3 June 2008

A repository of assays to quantify 10,000 human proteins by SWATH-MS.

scientific article

A systematic approach to modeling, capturing, and disseminating proteomics experimental data

scientific article

A tissue-based draft map of the murine MHC class I immunopeptidome

article by Heiko Schuster et al published 7 August 2018 in Scientific Data

ATAQS: A computational software tool for high throughput transition optimization and validation for selected reaction monitoring mass spectrometry ⬇️

scientific article published on March 18, 2011

Advances in Identifying and Characterizing the Human Proteome

scientific article published on 01 December 2019

An Open Data Format for Visualization and Analysis of Cross-Linked Mass Spectrometry Results

scientific article

An open-source computational and data resource to analyze digital maps of immunopeptidomes

scientific article

Analysis of the Saccharomyces cerevisiae proteome with PeptideAtlas

scientific article published on January 2006

Annual spring meeting of the Proteomics Standards Initiative

scientific article published in October 2009

Annual spring meeting of the Proteomics Standards Initiative 23-25 April 2008, Toledo, Spain

scientific article published in October 2008

Artificial decoy spectral libraries for false discovery rate estimation in spectral library searching in proteomics

scientific article

BDQC: a general-purpose analytics tool for domain-blind validation of Big Data

Big biomedical data as the key resource for discovery science

scientific article published on 21 July 2015

BioHackathon 2015: Semantics of data for life sciences and reproducible research

scientific article published on 24 February 2020

Biolink Model: A Universal Schema for Knowledge Graphs in Clinical, Biomedical, and Translational Science ⬇️

scientific article

Building ProteomeTools based on a complete synthetic human proteome

scientific article

Building consensus spectral libraries for peptide identification in proteomics

scientific article

Combining results of multiple search engines in proteomics

scientific article published on 29 May 2013

Comprehensive de novo structure prediction in a systems-biology context for the archaea Halobacterium sp. NRC-1

scientific article

Controlled vocabularies and ontologies in proteomics: overview, principles and practice

scientific article

Correlation of mRNA and protein levels: cell type-specific gene expression of cluster designation antigens in the prostate

scientific article

Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics

scientific article

Data standards for Omics data: the basis of data sharing and reuse

scientific article (publication date: 2011)

Design and implementation of microarray gene expression markup language (MAGE-ML)

scientific article

Development and validation of a spectral library searching method for peptide identification from MS/MS.

scientific article published in March 2007

Development of data representation standards by the human proteome organization proteomics standards initiative

scientific article

Development of the Minimum Information Specification for In Situ Hybridization and Immunohistochemistry Experiments (MISFISHIE).

scientific article published on January 2006

Discovering and linking public omics data sets using the Omics Discovery Index.

scientific article

Enabling BioSharing - a report on the Annual Spring Workshop of the HUPO-PSI April 11-13, 2011, EMBL-Heidelberg, Germany

scientific article

Erratum: Corrigendum: A HUPO test sample study reveals common problems in mass spectrometry–based proteomics

scholarly article published in Nature Methods

Expanding the use of spectral libraries in proteomics

Fast and simple comparison of semi-structured data, with emphasis on electronic health records

article

File Formats Commonly Used in Mass Spectrometry Proteomics ⬇️

scientific article published on September 6, 2012

Five years of progress in the Standardization of Proteomics Data 4th Annual Spring Workshop of the HUPO-Proteomics Standards Initiative April 23-25, 2007 Ecole Nationale Supérieure (ENS), Lyon, France

scientific article

Flexible and Fast Mapping of Peptides to a Proteome with ProteoMapper

From proteomics data representation to public data flow: a report on the HUPO-PSI workshop September 2011, Geneva, Switzerland

scientific article published on February 2012

Genome sequence of Haloarcula marismortui: a halophilic archaeon from the Dead Sea

scientific article

Guidelines for reporting the use of mass spectrometry in proteomics.

scientific article

Halobacterium salinarum NRC-1 PeptideAtlas: toward strategies for targeted proteomics and improved proteome coverage

scientific article published on 25 July 2008

Highlights of the Biology and Disease-driven Human Proteome Project, 2015-2016.

scientific article published on 30 August 2016

Human Plasma PeptideAtlas

scientific article published on August 2005

Human Proteinpedia enables sharing of human protein data

scientific article

Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 2.1.

scientific article

Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 3.0.

scientific article published on 21 October 2019

Human SRMAtlas: A Resource of Targeted Assays to Quantify the Complete Human Proteome

scientific article

Hydra: a scalable proteomic search engine which utilizes the Hadoop distributed computing framework

scientific article

I'll take that to go: Big data bags and minimal identifiers for exchange of large, complex datasets

Implementing data standards: a report on the HUPOPSI workshop September 2009, Toronto, Canada

scientific article published in May 2010

Improving mass and liquid chromatography based identification of proteins using bayesian scoring

scientific article

Integration with the human genome of peptide sequences obtained by high-throughput mass spectrometry

scientific article

MaRiMba: a software application for spectral library-based MRM transition list assembly

scientific article

Mapping genetic variations to three-dimensional protein structures to enhance variant interpretation: a proposed framework

scientific article published on 18 December 2017

Mass Spectrometry-Based Plasma Proteomics: Considerations from Sample Collection to Achieving Translational Data

scientific article published on 11 October 2019

Mass spectrometer output file format mzML

scientific article (publication date: 2010)

Meeting new challenges: The 2014 HUPO-PSI/COSMOS Workshop: 13-15 April 2014, Frankfurt, Germany

scientific article published on 9 October 2014

Meta-Analysis of Rice Phosphoproteomics Data to Understand Variation in Cell Signaling Across the Rice Pan-Genome

scientific article published in 2024

Metrics for the Human Proteome Project 2013-2014 and strategies for finding missing proteins

scientific article

Metrics for the Human Proteome Project 2015: Progress on the Human Proteome and Guidelines for High-Confidence Protein Identification

scientific article

Metrics for the Human Proteome Project 2016: Progress on Identifying and Characterizing the Human Proteome, Including Post-Translational Modifications

scientific article published on 03 August 2016

Mining PeptideAtlas for biomarkers and therapeutics in human disease

scientific article

Numerical compression schemes for proteomics mass spectrometry data

scientific article

Omics Discovery Index - Discovering and Linking Public Omics Datasets

Optical Identification of the X-Ray Burster X1746−370 in the Globular Cluster NGC 6441

scientific article published in Astronomical Journal

PASSEL: The PeptideAtlas SRMexperiment library ⬇️

scientific article published on April 1, 2012

PTMProphet: Fast and Accurate Mass Modification Localization for the Trans-Proteomic Pipeline

scientific article published on 22 July 2019

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

scientific article published on May 2008

Predictive Big Data Analytics: A Study of Parkinson's Disease Using Large, Complex, Heterogeneous, Incongruent, Multi-Source and Incomplete Observations

scientific article

Preparing to work with big data in proteomics - a report on the HUPO-PSI Spring Workshop: April 15-17, 2013, Liverpool, UK.

scientific article published in October 2013

Processing shotgun proteomics data on the Amazon cloud with the trans-proteomic pipeline

scientific article

Profiling the Human Phosphoproteome to Estimate the True Extent of Protein Phosphorylation

scientific article published on 09 May 2022

Progress and Future Direction of Chromosome-Centric Human Proteome Project

scientific article published in December 2017

Progress in the Chromosome-Centric Human Proteome Project as Highlighted in the Annual Special Issue IV.

scientific article

Progress on Identifying and Characterizing the Human Proteome: 2018 Metrics from the HUPO Human Proteome Project

scientific article published on 23 August 2018

Progress on Identifying and Characterizing the Human Proteome: 2019 Metrics from the HUPO Human Proteome Project

scientific article published on 13 September 2019

Progress on the HUPO Draft Human Proteome: 2017 Metrics of the Human Proteome Project.

scientific article published on 30 August 2017

Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project

scientific article (publication date: August 2008)

Proteome-wide cellular protein concentrations of the human pathogen Leptospira interrogans

scientific article published on 15 July 2009

ProteomeXchange provides globally coordinated proteomics data submission and dissemination

scientific article (publication date: March 2014)

Proteomics Standards Initiative Extended FASTA Format

scientific article published on 23 May 2019

Proteomics Standards Initiative's ProForma 2.0: Unifying the Encoding of Proteoforms and Peptidoforms

scientific article published on 15 March 2022

Recent Advances in the Chromosome-Centric Human Proteome Project: Missing Proteins in the Spot Light

article

Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam Principles)

scientific article

Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam Principles).

scientific article published on 3 November 2011

Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam principles).

scientific article published on 14 December 2011

Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam principles).

scientific article published in December 2011

Reproducible big data science: A case study in continuous FAIRness

scholarly article published 27 February 2018

Reproducible quantification of cancer-associated proteins in body fluids using targeted proteomics

scientific article

SBEAMS-Microarray: database software supporting genomic expression analyses for systems biology

scientific article published on 6 June 2006

Spectra, Chromatograms, Metadata: mzML-The Standard Data Format for Mass Spectrometer Output ⬇️

scientific article published on January 1, 2011

State of the Human Proteome in 2014/2015 As Viewed through PeptideAtlas: Enhancing Accuracy and Coverage through the AtlasProphet

scientific article published on 3 July 2015

State of the human proteome in 2013 as viewed through PeptideAtlas: comparing the kidney, urine, and plasma proteomes for the biology- and disease-driven Human Proteome Project

scientific article published on 06 December 2013

Tandem Mass Spectrometry Spectral Libraries and Library Searching ⬇️

scientific article published on January 1, 2011

Targeted quantitative analysis of Streptococcus pyogenes virulence factors by multiple reaction monitoring

scientific article published on 13 April 2008

Ten years of standardizing proteomic data: a report on the HUPO-PSI Spring Workshop: April 12-14th, 2012, San Diego, USA

scientific article (publication date: September 2012)

The Chromosome-Centric Human Proteome Project for cataloging proteins encoded in the genome.

scientific article

The Drosophila melanogaster PeptideAtlas facilitates the use of peptide data for improved fly proteomics and genome annotation

scientific article

The Equine PeptideAtlas: a resource for developing proteomics-based veterinary research

scientific article

The HUPO initiative on Model Organism Proteomes, iMOP.

scientific article published in February 2012

The HUPO proteomics standards initiative- mass spectrometry controlled vocabulary

scientific article (publication date: 2013)

The Human Immunopeptidome Project: A Roadmap to Predict and Treat Immune Diseases

scientific article published on 19 November 2019

The Human Plasma Proteome Draft of 2017: Building on the Human Plasma PeptideAtlas from Mass Spectrometry and Complementary Assays

scientific article

The PeptideAtlas Project

scientific article

The PeptideAtlas project

scientific article

The ProteomeXchange consortium in 2017: supporting the cultural change in proteomics public data deposition

scientific article

The ProteomeXchange consortium in 2020: enabling 'big data' approaches in proteomics

scientific article published on 01 January 2020

The Proteomics Standards Initiative: Fifteen Years of Progress and Future Work.

scientific article

The State of the Human Proteome in 2012 as Viewed through PeptideAtlas ⬇️

scientific article published on 05 December 2012

The SysteMHC Atlas project

scientific article published on 29 July 2017

The human proteome project: Current state and future direction

scientific article published on 29 April 2011

The mzIdentML data standard for mass spectrometry-based proteomics results

scientific article (publication date: July 2012)

The mzIdentML data standard version 1.2, supporting advances in proteome informatics.

scientific article

The proBAM and proBed standard formats: enabling a seamless integration of genomics and proteomics data

scientific article published on 31 January 2018

The proBAM and proBed standard formats: enabling a seamless integration of genomics and proteomics data

The structure of the inner eastern spiral arm of M83

scientific article published in Astronomical Journal

The urologic epithelial stem cell database (UESC) - a web tool for cell type-specific gene expression and immunohistochemistry images of the prostate and bladder

scientific article

Tiered Human Integrated Sequence Search Databases for Shotgun Proteomics

scientific article published on 31 August 2016

Toward Completion of the Human Proteome Parts List: Progress Uncovering Proteins That Are Missing or Have Unknown Function and Developing Analytical Methods

scientific article published on 01 December 2018

TraML--a standard format for exchange of selected reaction monitoring transition lists

scientific article published on 12 December 2011

Trans-Proteomic Pipeline supports and improves analysis of electron transfer dissociation data sets

scientific article

Trans-Proteomic Pipeline, a standardized data processing pipeline for large-scale reproducible proteomics informatics

scientific article

Universal Spectrum Identifier for mass spectra

scientific article published on 28 June 2021

Using PeptideAtlas, SRMAtlas, and PASSEL: Comprehensive Resources for Discovery and Targeted Proteomics

scientific article

Using the Human Plasma PeptideAtlas to Study Human Plasma Proteins ⬇️

scientific article published on January 1, 2011

Visual proteomics of the human pathogen Leptospira interrogans

scientific article

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

scientific article

jTraML: an open source Java API for TraML, the PSI standard for sharing SRM transitions

scientific article published on 13 October 2011

mspecLINE: bridging knowledge of human disease with the proteome

scientific article

mzML--a community standard for mass spectrometry data

2011 scientific article

reSpect: software for identification of high and low abundance ion species in chimeric tandem mass spectra

scientific article published on 29 September 2015

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