Evidence map›Paper›PMID 27546229›Full record

ArticleProteomics2016

ProteinProcessor: A probabilistic analysis using mass accuracy and the MS spectrum.

Jonathan A Epstein, Paul S Blank, Brian C Searle, Aaron D Catlin, Stephanie M Cologna, Matthew T Olson, Peter S Backlund, Jens R Coorssen, Alfred L Yergey

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Proteomics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing papers in PubMed
–field-weighted citation impact
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

3 citing papers in PubMed.

  1. Review
  2. Review
  3. Alfred L. Yergey III (September 17, 1941-May 27, 2018).Journal of the American Society for Mass Spectrometry · 2019
    Article
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

9 authors.

Jonathan A EpsteinEunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, USA.
Paul S BlankSection on Integrative Biophysics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, USA.
Brian C SearleProteome Software Inc, Portland, OR, USA.
Aaron D CatlinEunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, USA.
Stephanie M ColognaDepartment of Chemistry, University of Illinois at Chicago, Chicago, IL, USA.
Matthew T OlsonDepartment of Pathology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA.
Peter S BacklundEunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, USA.
Jens R CoorssenFaculty of Graduate Studies and the Departments of Health Sciences and Biological Sciences, Brock University, St. Catharines, ON, Canada.
Alfred L YergeyEunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, USA. aly@helix.nih.gov.

Funding

Mechanisms and Intracellular Components in Exocytosis, Membrane Assembly and Repair, and Parasite ReplicationZIAHD001415 · NICHD · EUNICE KENNEDY SHRIVER NATIONAL INSTITUTE OF CHILD HEALTH & HUMAN DEVELOPMENT · PI ZIMMERBERG, JOSHUA · 2009 to 2025
$26.0M
Characterization Of Proteins By Mass SpectrometryZICHD001421 · NICHD · EUNICE KENNEDY SHRIVER NATIONAL INSTITUTE OF CHILD HEALTH & HUMAN DEVELOPMENT · PI STRATAKIS, CONSTANTINE A. · 2009 to 2018
$9.6M
CHARACTERIZATION OF PROTEINS BY MASS SPECTROMETRYZ01HD001421 · NICHD · EUNICE KENNEDY SHRIVER NATIONAL INSTITUTE OF CHILD HEALTH & HUMAN DEVELOPMENT · PI YERGEY, ALFRED L · 1998 to 2008
$1.3M
ENERGETICS OF THE INTERACTION BETWEEN WATER, MEMBRANES, AND MACROMOLECULESZ01HD001417 · NICHD · CHILD HEALTH AND HUMAN DEVELOPMENT · PI YERGEY, ALFRED L · 1994 to 2007
$50k
Intramural NIH HHS Z01 HD001417Intramural NIH HHS Z01 HD001421
6 · The paper itself

Abstract

Current approaches to protein identification rely heavily on database matching of fragmentation spectra or precursor peptide ions. We have developed a method for MALDI TOF-TOF instrumentation that uses peptide masses and their measurement errors to confirm protein identifications from a first pass MS/MS database search. The method uses MS1-level spectral data that have heretofore been ignored by most search engines. This approach uses the distribution of mass errors of peptide matches in the MS1 spectrum to develop a probability model that is independent of the MS/MS database search identifications. Peptide mass matches can come from both precursor ions that have been fragmented as well as those that are tentatively identified by accurate mass alone. This additional corroboration enables us to confirm protein identifications to MS/MS-based scores that are otherwise considered to be only of moderate quality. Straightforward and easily applicable to current proteomic analyses, this tool termed "ProteinProcessor" provides a robust and invaluable addition to current protein identification tools.

Indexed as

AlgorithmsAnimalsDatabases, ProteinHumansMiceModels, StatisticalPeptide MappingProteomicsSpectrometry, Mass, Matrix-Assisted Laser Desorption-IonizationTandem Mass SpectrometryBayesian analysisBioinformaticsMALDIProtein sequencingTandem mass spectrometry

Identifiers

PMID27546229
PMCPMC5176252

What OpenQuestion holds

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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.