Evidence map›Paper›PMID 25712262›Full record

ArticleGenomics, proteomics & bioinformatics2015

YPED: an integrated bioinformatics suite and database for mass spectrometry-based proteomics research.

Christopher M Colangelo, Mark Shifman, Kei-Hoi Cheung, Kathryn L Stone, Nicholas J Carriero, Erol E Gulcicek, TuKiet T Lam, Terence Wu, Robert D Bjornson, Can Bruce and 4 more

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Genomics, proteomics & bioinformatics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.

0numbers the graph read from it
0cells of the map it votes in
9citing papers in PubMed
2.4field-weighted citation impact, top 12% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

9 citing papers in PubMed, 17 citations in OpenAlex.

  1. Article
  2. Article
  3. Article
  4. Article
  5. Article
  6. Article
  7. Article
  8. Article
  9. Web resources for mass spectrometry-based proteomics.Genomics, proteomics & bioinformatics · 2015
    Review
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

14 authors at 2 institutions in 1 country.

Christopher M ColangeloW.M. Keck Foundation Biotechnology Resource Laboratory, School of Medicine, Yale University, New Haven, CT 06510, USA; Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06520, USA. Electronic address: christopher.colangelo@yale.edu.
Mark ShifmanYale Center for Medical Informatics, School of Medicine, Yale University, New Haven, CT 06510, USA; Department of Anesthesiology, School of Medicine, Yale University, New Haven, CT 06510, USA.
Kei-Hoi CheungYale Center for Medical Informatics, School of Medicine, Yale University, New Haven, CT 06510, USA; Department of Emergency Medicine, School of Medicine, Yale University, New Haven, CT 06510, USA; VA Connecticut Healthcare System, West Haven, CT 06516, USA.
Kathryn L StoneW.M. Keck Foundation Biotechnology Resource Laboratory, School of Medicine, Yale University, New Haven, CT 06510, USA; Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06520, USA.
Nicholas J CarrieroW.M. Keck Foundation Biotechnology Resource Laboratory, School of Medicine, Yale University, New Haven, CT 06510, USA; Department of Computer Science, Yale University, New Haven, CT 06520, USA; Yale Center for Genome Analysis, West Campus, Yale University, Orange, CT 06477, USA.
Erol E GulcicekW.M. Keck Foundation Biotechnology Resource Laboratory, School of Medicine, Yale University, New Haven, CT 06510, USA; Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06520, USA.
TuKiet T LamW.M. Keck Foundation Biotechnology Resource Laboratory, School of Medicine, Yale University, New Haven, CT 06510, USA; Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06520, USA.
Terence WuW.M. Keck Foundation Biotechnology Resource Laboratory, School of Medicine, Yale University, New Haven, CT 06510, USA; Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06520, USA; Yale West Campus Analytical Core, West Campus, Yale University, West Haven, CT 06516, USA.
Robert D BjornsonW.M. Keck Foundation Biotechnology Resource Laboratory, School of Medicine, Yale University, New Haven, CT 06510, USA; Department of Computer Science, Yale University, New Haven, CT 06520, USA; Yale Center for Genome Analysis, West Campus, Yale University, Orange, CT 06477, USA.
Can BruceW.M. Keck Foundation Biotechnology Resource Laboratory, School of Medicine, Yale University, New Haven, CT 06510, USA; Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06520, USA; Yale Bioinformatics Resource, School of Medicine, Yale University, New Haven, CT 06510, USA.
Angus C NairnDepartment of Psychiatry, School of Medicine, Yale University, New Haven, CT 06510, USA.
Jesse RinehartDepartment of Cellular & Molecular Physiology, School of Medicine, Yale University, New Haven, CT 06510, USA; Systems Biology Institute, Yale University, West Haven, CT 06516, USA.
Perry L MillerYale Center for Medical Informatics, School of Medicine, Yale University, New Haven, CT 06510, USA; Department of Anesthesiology, School of Medicine, Yale University, New Haven, CT 06510, USA; VA Connecticut Healthcare System, West Haven, CT 06516, USA.
Kenneth R WilliamsW.M. Keck Foundation Biotechnology Resource Laboratory, School of Medicine, Yale University, New Haven, CT 06510, USA; Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06520, USA.
W. M. Keck Foundation · USYale University · US

Funding

YALE UNIVERSITY CLINICAL AND TRANSLATIONAL SCIENCE AWARD PROGRAMUL1RR024139 · NCRR · YALE UNIVERSITY · PI SHERWIN, ROBERT S · 2006 to 2011
$56.8M
Yale/NIDA Neuroproteomics Research CenterP30DA018343 · NIDA · YALE UNIVERSITY · PI Marina R Picciotto · 2004 to 2026
$37.1M
Yale Alzheimer Disease Research CenterP50AG047270 · NIA · YALE UNIVERSITY · PI STRITTMATTER, STEPHEN M · 2015 to 2019
$8.3M
Investigation of Electrolyte Homeostasis via Quantitative ProteomicsK01DK089006 · NIDDK · YALE UNIVERSITY · PI RINEHART, JESSE · 2010 to 2014
$772k
6500 QTrap Mass Spectrometer for Yale UniversityS10OD018034 · OD · YALE UNIVERSITY · PI MANE, SHRIKANT M · 2014 to 2014
$514k
5500 QTrap Mass Spectrometer for Yale University, Keck LaboratoryS10RR026707 · NCRR · YALE UNIVERSITY · PI COLANGELO, CHRISTOPHER MICHAEL · 2010 to 2010
$492k
NCRR NIH HHS 1S10RR026707-01NCRR NIH HHS S10 RR026707NCRR NIH HHS UL1 RR024139NIA NIH HHS P50 AG047270NIDA NIH HHS P30 DA018343NIDA NIH HHS P30DA018343NIDDK NIH HHS K01 DK089006NIH HHS 1S10OD018034-01NIH HHS S10 OD018034PHS HHS NIDDK-K01DK089006
6 · The paper itself

Abstract

We report a significantly-enhanced bioinformatics suite and database for proteomics research called Yale Protein Expression Database (YPED) that is used by investigators at more than 300 institutions worldwide. YPED meets the data management, archival, and analysis needs of a high-throughput mass spectrometry-based proteomics research ranging from a single laboratory, group of laboratories within and beyond an institution, to the entire proteomics community. The current version is a significant improvement over the first version in that it contains new modules for liquid chromatography-tandem mass spectrometry (LC-MS/MS) database search results, label and label-free quantitative proteomic analysis, and several scoring outputs for phosphopeptide site localization. In addition, we have added both peptide and protein comparative analysis tools to enable pairwise analysis of distinct peptides/proteins in each sample and of overlapping peptides/proteins between all samples in multiple datasets. We have also implemented a targeted proteomics module for automated multiple reaction monitoring (MRM)/selective reaction monitoring (SRM) assay development. We have linked YPED's database search results and both label-based and label-free fold-change analysis to the Skyline Panorama repository for online spectra visualization. In addition, we have built enhanced functionality to curate peptide identifications into an MS/MS peptide spectral library for all of our protein database search identification results.

Indexed as

Databases, ProteinChromatography, LiquidComputational BiologyHumansPeptide FragmentsProteomeProteomicsTandem Mass SpectrometryPeptide FragmentsProteomeBioinformaticsDatabaseMass spectrometryProteomicsRepositorySpectral library

Identifiers

PMID25712262
PMCPMC4411476
OpenAlexW2095070255

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.