Exploring the potential of public proteomics data (Q26785886)

7

0 references

Lennart Martens

6

object named as

Lennart Martens

0 references

Harald Barsnes

8

object named as

Harald Barsnes

0 references

author name string

Marc Vaudel

1

0 references

Attila Csordas

3

0 references

Helge Raeder

4

0 references

Frode S Berven

Creative Commons Attribution

5

0 references

language of work or name

English

0 references

publication date

January 2016

0 references

1 January 2016

1 reference

25 November 2020

1 reference

25 November 2020

16

0 references

page(s)

214-25

0 references

issue

2

0 references

copyright license

1 reference

25 November 2020

0 references

Updates to BioSamples database at European Bioinformatics Institute

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4738454

NCBI GEO: archive for functional genomics data sets--update

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4738454

A cross-platform toolkit for mass spectrometry and proteomics

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4738454

MOPED: Model Organism Protein Expression Database

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4738454

neXtProt: a knowledge platform for human proteins

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4738454

The effect of using an inappropriate protein database for proteomic data analysis

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4738454

Iridovirus and microsporidian linked to honey bee colony decline

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4738454

A probability-based approach for high-throughput protein phosphorylation analysis and site localization

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4738454

7 April 2017

The PeptideAtlas project

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4738454

Status of large-scale analysis of post-translational modifications by mass spectrometry

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4738454

Identifying novel biomarkers through data mining-a realistic scenario?

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4738454

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

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4738454

PhosphoSitePlus, 2014: mutations, PTMs and recalibrations

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4738454

Multiple evidence strands suggest that there may be as few as 19,000 human protein-coding genes

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4738454

Global quantification of mammalian gene expression control

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4738454

Protein sequences from mastodon and Tyrannosaurus rex revealed by mass spectrometry

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4738454

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

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4738454

Proteogenomics: concepts, applications and computational strategies

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4738454

Making proteomics data accessible and reusable: current state of proteomics databases and repositories

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4738454

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

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4738454

Tools (Viewer, Library and Validator) that facilitate use of the peptide and protein identification standard format, termed mzIdentML

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4738454

The MetaboLights repository: curation challenges in metabolomics

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4738454

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

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4738454

The mzQuantML data standard for mass spectrometry-based quantitative studies in proteomics

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4738454

The Online Protein Processing Resource (TOPPR): a database and analysis platform for protein processing events

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4738454

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

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4738454

The mzIdentML data standard for mass spectrometry-based proteomics results

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4738454

PRIDE Inspector: a tool to visualize and validate MS proteomics data

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4738454

Published and perished? The influence of the searched protein database on the long-term storage of proteomics data

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4738454

mzML--a community standard for mass spectrometry data

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4738454

Reanalysis of Tyrannosaurus rex Mass Spectra

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4738454

Comment on "Protein sequences from mastodon and Tyrannosaurus rex revealed by mass spectrometry"

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4738454

Reuse of public genome-wide gene expression data

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4738454

Proteomics. Tissue-based map of the human proteome

7 April 2017

3 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4738454

7 April 2017

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4738454

28 November 2018

12 December 2020

Mass-spectrometry-based draft of the human proteome

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4738454

A draft map of the human proteome

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4738454

ProteomeXchange provides globally coordinated proteomics data submission and dissemination

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4738454

BioMart--biological queries made easy

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4738454

The universal protein resource (UniProt)

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4738454

The minimum information about a proteomics experiment (MIAPE)

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4738454

TANDEM: matching proteins with tandem mass spectra

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4738454

Proteogenomic analysis of psoriasis reveals discordant and concordant changes in mRNA and protein abundance.

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4738454

An extensive library of surrogate peptides for all human proteins.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4738454

Mass spectrometrists should search only for peptides they care about

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4738454

Honey Bee Infecting Lake Sinai Viruses.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4738454

A mass-tolerant database search identifies a large proportion of unassigned spectra in shotgun proteomics as modified peptides

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4738454

Quest for Missing Proteins: Update 2015 on Chromosome-Centric Human Proteome Project

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4738454

Alternatively Spliced Homologous Exons Have Ancient Origins and Are Highly Expressed at the Protein Level.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4738454

Introducing the PRIDE Archive RESTful web services

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4738454

28 September 2017

The GPMDB REST interface

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4738454

Version 4.0 of PaxDb: Protein abundance data, integrated across model organisms, tissues, and cell-lines.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4738454

PROTEOFORMER: deep proteome coverage through ribosome profiling and MS integration

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4738454

Viewing the proteome: how to visualize proteomics data?

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4738454

LuciPHOr2: site localization of generic post-translational modifications from tandem mass spectrometry data.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4738454

Beyond protein expression, MOPED goes multi-omics

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4738454

A proteogenomics approach integrating proteomics and ribosome profiling increases the efficiency of protein identification and enables the discovery of alternative translation start sites

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4738454

Panorama: a targeted proteomics knowledge base

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4738454

SpliceVista, a tool for splice variant identification and visualization in shotgun proteomics data

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4738454

MS-viewer: a web-based spectral viewer for proteomics results

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4738454

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

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4738454

Recent advances in mass spectrometry: data independent analysis and hyper reaction monitoring

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4738454

LuciPHOr: algorithm for phosphorylation site localization with false localization rate estimation using modified target-decoy approach

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4738454

A Candida albicans PeptideAtlas

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4738454

Getting intimate with trypsin, the leading protease in proteomics

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4738454

Phosphoproteomics--more than meets the eye.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4738454

Scholarship: Beyond the paper

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4738454

Predicting tryptic cleavage from proteomics data using decision tree ensembles

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4738454

Crowdsourcing in proteomics: public resources lead to better experiments

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4738454

PRIDE Cluster: building a consensus of proteomics data

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4738454

Current methods for global proteome identification

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4738454

Protein structure as a means to triage proposed PTM sites

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4738454

Discovery of O-GlcNAc-6-phosphate modified proteins in large-scale phosphoproteomics data

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4738454

pep2pro: the high-throughput proteomics data processing, analysis, and visualization tool

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4738454

PaxDb, a database of protein abundance averages across all three domains of life

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4738454

Comparative proteomics reveals a significant bias toward alternative protein isoforms with conserved structure and function

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4738454

Modification site localization scoring: strategies and performance

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4738454

PASSEL: the PeptideAtlas SRMexperiment library

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4738454

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

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4738454

Spectral archives: extending spectral libraries to analyze both identified and unidentified spectra

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4738454

Shotgun proteomics aids discovery of novel protein-coding genes, alternative splicing, and "resurrected" pseudogenes in the mouse genome

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4738454

Interpretation of data underlying the link between colony collapse disorder (CCD) and an invertebrate iridescent virus

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4738454

A global analysis of peptide fragmentation variability

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4738454

Confident phosphorylation site localization using the Mascot Delta Score

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4738454

TOPPView: an open-source viewer for mass spectrometry data

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4738454

The proteios software environment: an extensible multiuser platform for management and analysis of proteomics data

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4738454

TB database: an integrated platform for tuberculosis research

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4738454

Comment on "Protein sequences from mastodon and Tyrannosaurus rex revealed by mass spectrometry".

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4738454

Peptizer, a tool for assessing false positive peptide identifications and manually validating selected results

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4738454

Clustering millions of tandem mass spectra

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4738454

Analyzing large-scale proteomics projects with latent semantic indexing

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4738454

Implementation and application of a versatile clustering tool for tandem mass spectrometry data

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4738454

MASPECTRAS: a platform for management and analysis of proteomics LC-MS/MS data

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4738454

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

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4738454

Analysis of peptide MS/MS spectra from large-scale proteomics experiments using spectrum libraries

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4738454

Overview of the HUPO Plasma Proteome Project: results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-available database

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4738454

PRIDE: the proteomics identifications database

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4738454

Do we want our data raw? Including binary mass spectrometry data in public proteomics data repositories

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4738454

Open source system for analyzing, validating, and storing protein identification data

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4738454

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

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4738454

Optimized nonlinear gradients for reversed-phase liquid chromatography in shotgun proteomics

31 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4738454

Reanalysis of phosphoproteomics data uncovers ADP-ribosylation sites

31 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4738454

MRMaid 2.0: mining PRIDE for evidence-based SRM transitions

31 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4738454

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

31 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4738454

PRIDE Converter: making proteomics data-sharing easy

31 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4738454

Interpreting sequences from mastodon and T. rex.

31 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4738454

On Credibility, Clarity, and Compliance.

31 May 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201500295

TopFIND, a knowledgebase linking protein termini with function.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201500295

PeptidePicker: a scientific workflow with web interface for selecting appropriate peptides for targeted proteomics experiments.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201500295

MS2PIP: a tool for MS/MS peak intensity prediction

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201500295

Analysis of the experimental detection of central nervous system-related genes in human brain and cerebrospinal fluid datasets

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201500295

BioMart: driving a paradigm change in biological data management

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201500295

MS2Grouper: group assessment and synthetic replacement of duplicate proteomic tandem mass spectra.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201500295

A spectral clustering approach to MS/MS identification of post-translational modifications

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201500295

Spectral archives: a vision for future proteomics data repositories

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201500295

A stringent approach to improve the quality of nitrotyrosine peptide identifications.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201500295

The biology/disease-driven human proteome project (B/D-HPP): enabling protein research for the life sciences community

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201500295

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201500295

PeptideShaker enables reanalysis of MS-derived proteomics data sets.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201500295

Distributed and interactive visual analysis of omics data

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201500295

Bromenshenk et al (PLoS One, 2011, 5(10):e13181) have claimed to have found peptides from an invertebrate iridovirus in bees

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201500295

Analyzing the first drafts of the human proteome.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201500295

Universal and confident phosphorylation site localization using phosphoRS.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201500295

D-score: a search engine independent MD-score.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201500295

Towards a human proteomics atlas

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201500295

Systematic and quantitative comparison of digest efficiency and specificity reveals the impact of trypsin quality on MS-based proteomics

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201500295

Why phosphoproteomics is still a challenge

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201500295

Democratizing proteomics data

21 January 2018

1 reference

PubMed

12 December 2020

Credit where credit is overdue

1 reference

PubMed

12 December 2020

An update on LNCipedia: a database for annotated human lncRNA sequences

1 reference

PubMed

12 December 2020