Lista de obras -

A Pipeline for Differential Proteomics in Unsequenced Species

artículo científico publicado en 2016

A Simple Workflow for Large Scale Shotgun Glycoproteomics.

artículo científico publicado en 2016

A global analysis of peptide fragmentation variability

artículo científico publicado en 2011

An Accessible Proteogenomics Informatics Resource for Cancer Researchers

artículo científico publicado en 2017

Analyzing the Structure of Pathways and Its Influence on the Interpretation of Biomedical Proteomics Data Sets

artículo científico publicado en 2018

Anatomy and evolution of database search engines-a central component of mass spectrometry based proteomic workflows

artículo científico publicado en 2017

BioContainers: An open-source and community-driven framework for software standardization

artículo científico publicado en 2017

Bioinformatics for proteomics: opportunities at the interface between the scientists, their experiments, and the community

scientific article published on 01 January 2014

Blind search for post-translational modifications and amino acid substitutions using peptide mass fingerprints from two proteases.

artículo científico publicado en 2008

CSF-PR 2.0: An Interactive Literature Guide to Quantitative Cerebrospinal Fluid Mass Spectrometry Data from Neurodegenerative Disorders

artículo científico publicado en 2016

Carboxyl-ester lipase maturity-onset diabetes of the young disease protein biomarkers in secretin-stimulated duodenal juice

scientific article published on 04 November 2014

Connecting MetaProteomeAnalyzer and PeptideShaker to Unipept for seamless end-to-end metaproteomics data analysis

scientific article published on 20 May 2020

Crowdsourcing in proteomics: public resources lead to better experiments

artículo científico publicado en 2013

Database Search Engines: Paradigms, Challenges and Solutions

artículo científico publicado en 2016

DeNovoGUI: an open source graphical user interface for de novo sequencing of tandem mass spectra.

artículo científico publicado en 2014

Detecting single amino acids and small peptides by combining isobaric tags and peptidomics

scientific article published on 12 June 2019

Development of robust targeted proteomics assays for cerebrospinal fluid biomarkers in multiple sclerosis

scientific article published on 18 September 2020

Discovery and initial verification of differentially abundant proteins between multiple sclerosis patients and controls using iTRAQ and SID-SRM ⬇️

artículo científico publicado el 8 de octubre de 2012

Distributed and interactive visual analysis of omics data

artículo científico publicado en 2015

Distributed computing and data storage in proteomics: many hands make light work, and a stronger memory

artículo científico publicado en 2013

Dynamic proteome profiling of human pluripotent stem cell-derived pancreatic progenitors

scientific article published on 22 January 2020

Erratum: ms_lims, a simple yet powerful open source laboratory information management system for MS-driven proteomics

scholarly article published in Proteomics

Essential Features and Use Cases of the Cerebrospinal Fluid Proteome Resource (CSF-PR)

scientific article published on 01 January 2019

Exploring the potential of public proteomics data

artículo científico publicado en 2016

FragmentationAnalyzer: an open-source tool to analyze MS/MS fragmentation data

artículo científico publicado en 2010

Getting a grip on proteomics data - Proteomics Data Collection (ProDaC).

artículo científico publicado en 2009

In-Depth Cerebrospinal Fluid Quantitative Proteome and Deglycoproteome Analysis: Presenting a Comprehensive Picture of Pathways and Processes Affected by Multiple Sclerosis

artículo científico publicado en 2016

In-depth characterization of the cerebrospinal fluid (CSF) proteome displayed through the CSF proteome resource (CSF-PR).

artículo científico publicado en 2014

Interpretation of Quantitative Shotgun Proteomic Data.

artículo científico publicado en 2016

IsobariQ: software for isobaric quantitative proteomics using IPTL, iTRAQ, and TMT.

artículo científico publicado en 2010

JSparklines: making tabular proteomics data come alive

artículo científico publicado en 2015

Label-free analysis of human cerebrospinal fluid addressing various normalization strategies and revealing protein groups affected by multiple sclerosis.

artículo científico publicado en 2016

Leptin Receptor Signaling Regulates Protein Synthesis Pathways and Neuronal Differentiation in Pluripotent Stem Cells

scientific article published on 20 October 2020

Machine learning applications in proteomics research: how the past can boost the future

artículo científico publicado en 2014

MassSorter: a tool for administrating and analyzing data from mass spectrometry experiments on proteins with known amino acid sequences.

artículo científico publicado en 2006

MassSorter: peptide mass fingerprinting data analysis.

artículo científico publicado en 2008

OLS Client and OLS Dialog: Open source tools to annotate public omics datasets.

artículo científico

OLS dialog: an open-source front end to the ontology lookup service

artículo científico publicado en 2010

OMSSA Parser: an open-source library to parse and extract data from OMSSA MS/MS search results

artículo científico publicado en 2009

On the importance of block randomisation when designing proteomics experiments

scientific article published on 21 September 2020

PRIDE Converter: making proteomics data-sharing easy

artículo científico publicado en 2009

PathwayMatcher: proteoform-centric network construction enables fine-granularity multiomics pathway mapping

artículo científico publicado en 2019

PeptideMapper: Efficient and Versatile Amino Acid Sequence and Tag Mapping

artículo científico publicado en 2017

PeptideShaker enables reanalysis of MS-derived proteomics data sets.

artículo científico publicado en 2015

Pladipus Enables Universal Distributed Computing in Proteomics Bioinformatics.

artículo científico

Practical Considerations for Omics Experiments in Biomedical Sciences.

artículo científico

Pride-asap: automatic fragment ion annotation of identified PRIDE spectra

artículo científico publicado en 2013

Protease-dependent fractional mass and peptide properties.

artículo científico publicado en 2008

Proteomics Data Collection - 5th ProDaC Workshop: 4 March 2009, Kolympari, Crete, Greece.

artículo científico publicado en 2009

Proteomics Data Visualisation

artículo científico publicado en 2015

Proteomics Standards Initiative Extended FASTA Format

artículo científico publicado en 2019

Proteomics data collection--4th ProDaC workshop 15 August 2008, Amsterdam, The Netherlands

artículo científico publicado en 2009

Quantitative proteomics suggests decrease in the secretogranin-1 cerebrospinal fluid levels during the disease course of multiple sclerosis

artículo científico publicado en 2015

SearchGUI: A Highly Adaptable Common Interface for Proteomics Search and de Novo Engines

scientific article published on 25 May 2018

SearchGUI: An open-source graphical user interface for simultaneous OMSSA and X!Tandem searches.

artículo científico publicado en 2011

Shedding light on black boxes in protein identification

artículo científico publicado en 2014

Submitting proteomics data to PRIDE using PRIDE Converter

artículo científico publicado en 2011

Systemic Analysis of Regulated Functional Networks.

artículo científico publicado en 2016

Tandem Mass Spectrum Sequencing: An Alternative to Database Search Engines in Shotgun Proteomics

artículo científico publicado en 2016

The Ontology Lookup Service: bigger and better

artículo científico publicado en 2010

The PRoteomics IDEntification (PRIDE) Converter 2 framework: an improved suite of tools to facilitate data submission to the PRIDE database and the ProteomeXchange consortium

artículo científico publicado en 2012

The Proteomics Identifications database: 2010 update

artículo científico publicado en 2010

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

artículo científico publicado en 2017

Thermo-msf-parser: an open source Java library to parse and visualize Thermo Proteome Discoverer msf files

artículo científico publicado en 2011

ThermoRawFileParser: Modular, Scalable, and Cross-Platform RAW File Conversion

scientific article published on 06 December 2019

Use of Stable Isotope Dimethyl Labeling Coupled to Selected Reaction Monitoring to Enhance Throughput by Multiplexing Relative Quantitation of Targeted Proteins

artículo científico publicado en 2012

Using Proteomics Bioinformatics Tools and Resources in Proteogenomic Studies.

artículo científico publicado en 2016

Viewing the proteome: how to visualize proteomics data?

artículo científico publicado en 2015

Visualization, Inspection and Interpretation of Shotgun Proteomics Identification Results

artículo científico publicado en 2016

XTandem Parser: an open-source library to parse and analyse X!Tandem MS/MS search results

artículo científico publicado en 2010

compomics-utilities: an open-source Java library for computational proteomics

artículo científico publicado en 2011

ms_lims, a simple yet powerful open source laboratory information management system for MS-driven proteomics.

artículo científico publicado en 2010

Lista de obras de

A Pipeline for Differential Proteomics in Unsequenced Species

A Simple Workflow for Large Scale Shotgun Glycoproteomics.

A global analysis of peptide fragmentation variability

An Accessible Proteogenomics Informatics Resource for Cancer Researchers

Analyzing the Structure of Pathways and Its Influence on the Interpretation of Biomedical Proteomics Data Sets

Anatomy and evolution of database search engines-a central component of mass spectrometry based proteomic workflows

BioContainers: An open-source and community-driven framework for software standardization

Bioinformatics for proteomics: opportunities at the interface between the scientists, their experiments, and the community

Blind search for post-translational modifications and amino acid substitutions using peptide mass fingerprints from two proteases.

CSF-PR 2.0: An Interactive Literature Guide to Quantitative Cerebrospinal Fluid Mass Spectrometry Data from Neurodegenerative Disorders

Carboxyl-ester lipase maturity-onset diabetes of the young disease protein biomarkers in secretin-stimulated duodenal juice

Connecting MetaProteomeAnalyzer and PeptideShaker to Unipept for seamless end-to-end metaproteomics data analysis

Crowdsourcing in proteomics: public resources lead to better experiments

Database Search Engines: Paradigms, Challenges and Solutions

DeNovoGUI: an open source graphical user interface for de novo sequencing of tandem mass spectra.

Detecting single amino acids and small peptides by combining isobaric tags and peptidomics

Development of robust targeted proteomics assays for cerebrospinal fluid biomarkers in multiple sclerosis

Discovery and initial verification of differentially abundant proteins between multiple sclerosis patients and controls using iTRAQ and SID-SRM ⬇️

Distributed and interactive visual analysis of omics data

Distributed computing and data storage in proteomics: many hands make light work, and a stronger memory

Dynamic proteome profiling of human pluripotent stem cell-derived pancreatic progenitors

Erratum: ms_lims, a simple yet powerful open source laboratory information management system for MS-driven proteomics

Essential Features and Use Cases of the Cerebrospinal Fluid Proteome Resource (CSF-PR)

Exploring the potential of public proteomics data

FragmentationAnalyzer: an open-source tool to analyze MS/MS fragmentation data

Getting a grip on proteomics data - Proteomics Data Collection (ProDaC).

In-Depth Cerebrospinal Fluid Quantitative Proteome and Deglycoproteome Analysis: Presenting a Comprehensive Picture of Pathways and Processes Affected by Multiple Sclerosis

In-depth characterization of the cerebrospinal fluid (CSF) proteome displayed through the CSF proteome resource (CSF-PR).

Interpretation of Quantitative Shotgun Proteomic Data.

IsobariQ: software for isobaric quantitative proteomics using IPTL, iTRAQ, and TMT.

JSparklines: making tabular proteomics data come alive

Label-free analysis of human cerebrospinal fluid addressing various normalization strategies and revealing protein groups affected by multiple sclerosis.

Leptin Receptor Signaling Regulates Protein Synthesis Pathways and Neuronal Differentiation in Pluripotent Stem Cells

Machine learning applications in proteomics research: how the past can boost the future

MassSorter: a tool for administrating and analyzing data from mass spectrometry experiments on proteins with known amino acid sequences.

MassSorter: peptide mass fingerprinting data analysis.

OLS Client and OLS Dialog: Open source tools to annotate public omics datasets.

OLS dialog: an open-source front end to the ontology lookup service

OMSSA Parser: an open-source library to parse and extract data from OMSSA MS/MS search results

On the importance of block randomisation when designing proteomics experiments

PRIDE Converter: making proteomics data-sharing easy

PathwayMatcher: proteoform-centric network construction enables fine-granularity multiomics pathway mapping

PeptideMapper: Efficient and Versatile Amino Acid Sequence and Tag Mapping

PeptideShaker enables reanalysis of MS-derived proteomics data sets.

Pladipus Enables Universal Distributed Computing in Proteomics Bioinformatics.

Practical Considerations for Omics Experiments in Biomedical Sciences.

Pride-asap: automatic fragment ion annotation of identified PRIDE spectra

Protease-dependent fractional mass and peptide properties.

Proteomics Data Collection - 5th ProDaC Workshop: 4 March 2009, Kolympari, Crete, Greece.

Proteomics Data Visualisation

Proteomics Standards Initiative Extended FASTA Format

Proteomics data collection--4th ProDaC workshop 15 August 2008, Amsterdam, The Netherlands

Quantitative proteomics suggests decrease in the secretogranin-1 cerebrospinal fluid levels during the disease course of multiple sclerosis

SearchGUI: A Highly Adaptable Common Interface for Proteomics Search and de Novo Engines

SearchGUI: An open-source graphical user interface for simultaneous OMSSA and X!Tandem searches.

Shedding light on black boxes in protein identification

Submitting proteomics data to PRIDE using PRIDE Converter

Systemic Analysis of Regulated Functional Networks.

Tandem Mass Spectrum Sequencing: An Alternative to Database Search Engines in Shotgun Proteomics

The Ontology Lookup Service: bigger and better

The PRoteomics IDEntification (PRIDE) Converter 2 framework: an improved suite of tools to facilitate data submission to the PRIDE database and the ProteomeXchange consortium

The Proteomics Identifications database: 2010 update

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

Thermo-msf-parser: an open source Java library to parse and visualize Thermo Proteome Discoverer msf files

ThermoRawFileParser: Modular, Scalable, and Cross-Platform RAW File Conversion

Use of Stable Isotope Dimethyl Labeling Coupled to Selected Reaction Monitoring to Enhance Throughput by Multiplexing Relative Quantitation of Targeted Proteins

Using Proteomics Bioinformatics Tools and Resources in Proteogenomic Studies.

Viewing the proteome: how to visualize proteomics data?

Visualization, Inspection and Interpretation of Shotgun Proteomics Identification Results

XTandem Parser: an open-source library to parse and analyse X!Tandem MS/MS search results

compomics-utilities: an open-source Java library for computational proteomics

ms_lims, a simple yet powerful open source laboratory information management system for MS-driven proteomics.