Evidence map›Paper›PMID 30714740›Full record

ArticleJournal of proteome research2019

Detecting Modifications in Proteomics Experiments with Param-Medic.

Damon H May, Kaipo Tamura, William S Noble

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Journal of proteome research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing 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

1 citing paper in PubMed.

  1. 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

3 authors.

Damon H MayDepartment of Genome Sciences , University of Washington , Seattle , Washington 98195 , United States.ORCID 0000-0001-6902-3153
Kaipo TamuraDepartment of Genome Sciences , University of Washington , Seattle , Washington 98195 , United States.
William S NobleDepartment of Genome Sciences , University of Washington , Seattle , Washington 98195 , United States.ORCID 0000-0001-7283-4715

Funding

Optimization and joint modeling for peptide detection by tandem mass spectrometryR01GM121818 · NIGMS · UNIVERSITY OF WASHINGTON · PI NOBLE, WILLIAM STAFFORD · 2017 to 2020
$1.3M
NIGMS NIH HHS R01 GM121818
6 · The paper itself

Abstract

Searching tandem mass spectra against a peptide database requires accurate knowledge of various experimental parameters, including machine settings and details of the sample preparation protocol. In some cases, such as in reanalysis of public data sets, this experimental metadata may be missing or inaccurate. We describe a method for automatically inferring the presence of various types of modifications, including stable-isotope and isobaric labeling and tandem mass tags as well as the enrichment of phosphorylated peptides, directly from a given set of mass spectra. We demonstrate the sensitivity and specificity of the proposed approach, and we provide open-source Python and C++ implementations in a new version of the software tool Param-Medic.

Indexed as

Isotope LabelingSoftwareTandem Mass SpectrometryDatabases, ProteinPhosphopeptidesProteomeProteomicsPhosphopeptidesProteomedatabase searchisobaric labelingmass spectrometryphosphorylationproteomicstandem mass tags

Identifiers

PMID30714740
PMCPMC6450762

What OpenQuestion holds

Textmetadata
LicenceTDM
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.