A guided tour of the Trans-Proteomic Pipeline (Q30497827)

6 October 2017

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title

A guided tour of the Trans-Proteomic Pipeline (English)

1 reference

6 October 2017

Alexey I. Nesvizhskii

13

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6 October 2017

5

Henry Lam

1 reference

6 October 2017

14

Ruedi Aebersold

1 reference

6 October 2017

11

Jimmy K Eng

1 reference

6 October 2017

1

Eric W Deutsch

1 reference

6 October 2017

9

Brian Pratt

1 reference

6 October 2017

4

Terry Farrah

1 reference

6 October 2017

3

David Shteynberg

1 reference

6 October 2017

6

Natalie Tasman

1 reference

6 October 2017

Luis Mendoza

2

1 reference

6 October 2017

Zhi Sun

7

1 reference

6 October 2017

Erik Nilsson

8

1 reference

6 October 2017

Bryan Prazen

10

1 reference

6 October 2017

Daniel B Martin

12

1 reference

6 October 2017

1 March 2010

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6 October 2017

1 reference

6 October 2017

10

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6 October 2017

6

1 reference

6 October 2017

1150-1159

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

6 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017125

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017125

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017125

Getting started in computational mass spectrometry-based proteomics

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017125

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017125

mzML: a single, unifying data format for mass spectrometer output

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017125

MRMer, an interactive open source and cross-platform system for data extraction and visualization of multiple reaction monitoring experiments

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017125

The protein information and property explorer: an easy-to-use, rich-client web application for the management and functional analysis of proteomic data

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017125

ProteoWizard: open source software for rapid proteomics tools development

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017125

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017125

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017125

DeconMSn: a software tool for accurate parent ion monoisotopic mass determination for tandem mass spectra

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017125

Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017125

Statistical validation of peptide identifications in large-scale proteomics using the target-decoy database search strategy and flexible mixture modeling

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017125

False discovery rates and related statistical concepts in mass spectrometry-based proteomics

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017125

YPED: a web-accessible database system for protein expression analysis.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017125

The standard protein mix database: a diverse data set to assist in the production of improved Peptide and protein identification software tools

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017125

Quantitative mass spectrometry in proteomics: a critical review

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017125

Stable isotope labeling by amino acids in cell culture for quantitative proteomics

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017125

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017125

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017125

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017125

TOPP--the OpenMS proteomics pipeline

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017125

General framework for developing and evaluating database scoring algorithms using the TANDEM search engine

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017125

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017125

A uniform proteomics MS/MS analysis platform utilizing open XML file formats

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017125

A perspective on the use of iTRAQ reagent technology for protein complex and profiling studies

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017125

Computational Proteomics Analysis System (CPAS): an extensible, open-source analytic system for evaluating and publishing proteomic data and high throughput biological experiments

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017125

PRIDE: the proteomics identifications database

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017125

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017125

Open mass spectrometry search algorithm

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017125

A tool to visualize and evaluate data obtained by liquid chromatography-electrospray ionization-mass spectrometry

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017125

High-performance peptide identification by tandem mass spectrometry allows reliable automatic data processing in proteomics.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017125

TANDEM: matching proteins with tandem mass spectra

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017125

Analysis, statistical validation and dissemination of large-scale proteomics datasets generated by tandem MS.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017125

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017125

A statistical model for identifying proteins by tandem mass spectrometry

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017125

The application of new software tools to quantitative protein profiling via isotope-coded affinity tag (ICAT) and tandem mass spectrometry: II. Evaluation of tandem mass spectrometry methodologies for large-scale protein analysis, and the applicatio

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017125

Tandem Mass Tags: A Novel Quantification Strategy for Comparative Analysis of Complex Protein Mixtures by MS/MS

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017125

Mass spectrometry-based proteomics

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017125

ProbID: a probabilistic algorithm to identify peptides through sequence database searching using tandem mass spectral data

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017125

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017125

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017125

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017125

Semisupervised model-based validation of peptide identifications in mass spectrometry-based proteomics.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017125

Automated identification of SUMOylation sites using mass spectrometry and SUMmOn pattern recognition software.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017125

Reporting protein identification data: the next generation of guidelines.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017125

InsPecT: identification of posttranslationally modified peptides from tandem mass spectra

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017125

Revised draft guidelines for proteomic data publication

26 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/20101611

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1002/PMIC.200900375

1 reference

release_kne6cirexvbphaqrmpmlfmye34

6 October 2017

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/kne6cirexvbphaqrmpmlfmye34

mapped directly with Wikidata item

24 November 2022

based on heuristic

1 reference

6 October 2017

1 reference