(Q36095680)

12 August 2017

Recognizing millions of consistently unidentified spectra across hundreds of shotgun proteomics datasets (English)

1 reference

12 August 2017

1 reference

1 reference

9

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27493588%20AND%20SRC:MED&resulttype=core&format=json

12 June 2020

Henning Hermjakob

10

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27493588%20AND%20SRC:MED&resulttype=core&format=json

12 June 2020

Juan Antonio Vizcaíno

12

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27493588%20AND%20SRC:MED&resulttype=core&format=json

12 June 2020

Johannes Griss

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27493588%20AND%20SRC:MED&resulttype=core&format=json

12 June 2020

Yasset Perez-Riverol

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27493588%20AND%20SRC:MED&resulttype=core&format=json

12 June 2020

David Tabb

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27493588%20AND%20SRC:MED&resulttype=core&format=json

12 June 2020

Jose A Dianes

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27493588%20AND%20SRC:MED&resulttype=core&format=json

12 June 2020

Noemi del-Toro

6

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27493588%20AND%20SRC:MED&resulttype=core&format=json

12 June 2020

Mathias Walzer

8

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27493588%20AND%20SRC:MED&resulttype=core&format=json

12 June 2020

author name string

Steve Lewis

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27493588%20AND%20SRC:MED&resulttype=core&format=json

12 June 2020

Marc Rurik

7

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27493588%20AND%20SRC:MED&resulttype=core&format=json

12 June 2020

Rui Wang

11

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27493588%20AND%20SRC:MED&resulttype=core&format=json

12 June 2020

publication date

27 June 2016

1 reference

12 August 2017

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27493588%20AND%20SRC:MED&resulttype=core&format=json

12 June 2020

volume

13

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27493588%20AND%20SRC:MED&resulttype=core&format=json

12 June 2020

issue

8

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27493588%20AND%20SRC:MED&resulttype=core&format=json

12 June 2020

page(s)

651-656

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27493588%20AND%20SRC:MED&resulttype=core&format=json

https://scigraph.springernature.com/pub.10.1038/nmeth.3902

12 June 2020

exact match

0 references

cites work

Cleaning out the Litterbox of Proteomic Scientists' Favorite Pet: Optimized Data Analysis Avoiding Trypsin Artifacts

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4968634

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

2 October 2017

1 reference

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2016 update of the PRIDE database and its related tools

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4968634

cl-dash: rapid configuration and deployment of Hadoop clusters for bioinformatics research in the cloud.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4968634

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4968634

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4968634

Design and development of a medical big data processing system based on Hadoop

2 October 2017

1 reference

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How to submit MS proteomics data to ProteomeXchange via the PRIDE database

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4968634

Macroporous reversed-phase separation of proteins combined with reversed-phase separation of phosphopeptides and tandem mass spectrometry for profiling the phosphoproteome of MDA-MB-231 cells

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4968634

ProteomeXchange provides globally coordinated proteomics data submission and dissemination

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4968634

Hunting for unexpected post-translational modifications by spectral library searching with tier-wise scoring

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4968634

Confident and sensitive phosphoproteomics using combinations of collision induced dissociation and electron transfer dissociation

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4968634

Environmental stress affects the activity of metabolic and growth factor signaling networks and induces autophagy markers in MCF7 breast cancer cells

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4968634

Chromosome-8-coded proteome of Chinese Chromosome Proteome Data set (CCPD) 2.0 with partial immunohistochemical verifications

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4968634

Sequential phosphoproteomic enrichment through complementary metal-directed immobilized metal ion affinity chromatography

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4968634

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4968634

Expanding tandem mass spectral libraries of phosphorylated peptides: advances and applications

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4968634

Deep proteome coverage based on ribosome profiling aids mass spectrometry-based protein and peptide discovery and provides evidence of alternative translation products and near-cognate translation initiation events

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4968634

PRIDE Cluster: building a consensus of proteomics data

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4968634

PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4968634

Data extraction from proteomics raw data: an evaluation of nine tandem MS tools using a large Orbitrap data set.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4968634

Pepitome: evaluating improved spectral library search for identification complementarity and quality assessment

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4968634

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4968634

Peptide identification from mixture tandem mass spectra

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4968634

Exploring the human leukocyte phosphoproteome using a microfluidic reversed-phase-TiO2-reversed-phase high-performance liquid chromatography phosphochip coupled to a quadrupole time-of-flight mass spectrometer

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4968634

DirecTag: accurate sequence tags from peptide MS/MS through statistical scoring

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4968634

OpenMS - an open-source software framework for mass spectrometry

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4968634

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4968634

2 October 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=4968634

PepNovo: de novo peptide sequencing via probabilistic network modeling

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4968634

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4968634

TANDEM: matching proteins with tandem mass spectra

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4968634

Mass spectrometry-based proteomics

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4968634

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4968634

Kinase-substrate enrichment analysis provides insights into the heterogeneity of signaling pathway activation in leukemia cells.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4968634

The use of mass defect in modern mass spectrometry.

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4968634

Spectral archives: a vision for future proteomics data repositories

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4968634

Quantitative erythrocyte membrane proteome analysis with Blue-native/SDS PAGE.

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4968634

23 September 2018

Identifiers

DOI

10.1038/NMETH.3902

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27493588%20AND%20SRC:MED&resulttype=core&format=json

12 June 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27493588%20AND%20SRC:MED&resulttype=core&format=json

12 June 2020

1 reference