Evidence map›Paper›PMID 33683901›Full record

ArticleJournal of proteome research2021

Binary Classifier for Computing Posterior Error Probabilities in MetaMorpheus.

Michael R Shortreed, Robert J Millikin, Lei Liu, Zach Rolfs, Rachel M Miller, Leah V Schaffer, Brian L Frey, Lloyd M Smith

Abstract read
In one paragraph

Article in Journal of proteome research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.

0numbers the graph read from it
0cells of the map it votes in
4citing 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

4 citing papers in PubMed.

  1. Article
  2. Article
  3. Article
  4. 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

8 authors.

Michael R ShortreedDepartment of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States.ORCID 0000-0003-4626-0863
Robert J MillikinDepartment of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States.ORCID 0000-0001-7440-3695
Lei LiuDepartment of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States.ORCID 0000-0001-7097-1505
Zach RolfsDepartment of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States.ORCID 0000-0002-4372-7133
Rachel M MillerDepartment of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States.ORCID 0000-0003-1461-6386
Leah V SchafferDepartment of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States.ORCID 0000-0001-6339-9141
Brian L FreyDepartment of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States.ORCID 0000-0002-0397-7269
Lloyd M SmithDepartment of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States.

Funding

BIOTECHNOLOGY TRAINING PROGRAMT32GM008349 · NIGMS · UNIVERSITY OF WISCONSIN-MADISON · PI FOX, BRIAN G · 1989 to 2019
$22.5M
Institutional Training in the Genomic SciencesT32HG002760 · NHGRI · UNIVERSITY OF WISCONSIN-MADISON · PI Qiongshi Lu · 2003 to 2026
$17.7M
Chemistry-Biology Interface Training ProgramT32GM008505 · NIGMS · UNIVERSITY OF WISCONSIN-MADISON · PI BLACKWELL, HELEN E. · 1993 to 2023
$9.8M
Revealing Proteoforms: The Primary Effectors of Biological FunctionR35GM126914 · NIGMS · UNIVERSITY OF WISCONSIN-MADISON · PI Lloyd M Smith · 2018 to 2026
$6.2M
NHGRI NIH HHS T32 HG002760NIGMS NIH HHS R35 GM126914NIGMS NIH HHS T32 GM008349NIGMS NIH HHS T32 GM008505
6 · The paper itself

Abstract

MetaMorpheus is a free, open-source software program for the identification of peptides and proteoforms from data-dependent acquisition tandem MS experiments. There is inherent uncertainty in these assignments for several reasons, including the limited overlap between experimental and theoretical peaks, the

Indexed as

ProteomicsTandem Mass SpectrometryAlgorithmsDatabases, ProteinPeptidesProbabilitySoftwarePeptidesbinary decision treebottom-upDDAMetaMorpheusopen sourceposterior error probabilityproteogenomicsproteomicssearch enginetop-down

Identifiers

PMID33683901
PMCPMC8377504

What OpenQuestion holds

Textmetadata
LicenceTDM
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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.