Evidence map›Paper›PMID 30591035›Full record

ArticleBMC bioinformatics2018

Evaluation of top-down mass spectral identification with homologous protein sequences.

Ziwei Li, Bo He, Qiang Kou, Zhe Wang, Si Wu, Yunlong Liu, Weixing Feng, Xiaowen Liu

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in BMC bioinformatics, 2018. 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

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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.

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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.

Ziwei LiCollege of Automation, Harbin Engineering University, 145, Nan Tong Street, Harbin, Heilongjiang, 150001, China.
Bo HeCollege of Automation, Harbin Engineering University, 145, Nan Tong Street, Harbin, Heilongjiang, 150001, China.
Qiang KouDepartment of BioHealth Informatics, Indiana University-Purdue University Indianapolis, 719 Indiana Avenue, Indianapolis, IN, 46202, USA.
Zhe WangDepartment of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA.
Si WuDepartment of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA.
Yunlong LiuDepartment of Medical and Molecular Genetics, Indiana University School of Medicine, 410 West 10th Street, Indianapolis, IN, 46202, USA. yunliu@iu.edu.
Weixing FengCollege of Automation, Harbin Engineering University, 145, Nan Tong Street, Harbin, Heilongjiang, 150001, China. fengweixing@hrbeu.edu.cn.
Xiaowen LiuDepartment of BioHealth Informatics, Indiana University-Purdue University Indianapolis, 719 Indiana Avenue, Indianapolis, IN, 46202, USA. xwliu@iupui.edu.

Funding

Computational tools for top down mass spectrometry based proteoform identification and proteogenomicsR01GM118470 · NIGMS · TULANE UNIVERSITY OF LOUISIANA · PI Xiaowen Liu · 2016 to 2026
$2.7M
Quantitative proteomics of Zebrafish embryos and blastomeresR01GM125991 · NIGMS · MICHIGAN STATE UNIVERSITY · PI SUN, LIANGLIANG · 2018 to 2022
$1.7M
NIGMS NIH HHS R01 GM118470NIGMS NIH HHS R01 GM125991
6 · The paper itself

Abstract

backgroundTop-down mass spectrometry has unique advantages in identifying proteoforms with multiple post-translational modifications and/or unknown alterations. Most software tools in this area search top-down mass spectra against a protein sequence database for proteoform identification. When the species studied in a mass spectrometry experiment lacks its proteome sequence database, a homologous protein sequence database can be used for proteoform identification. The accuracy of homologous protein sequences affects the sensitivity of proteoform identification and the accuracy of mass shift localization.

resultsWe tested TopPIC, a commonly used software tool for top-down mass spectral identification, on a top-down mass spectrometry data set of Escherichia coli K12 MG1655, and evaluated its performance using an Escherichia coli K12 MG1655 proteome database and a homologous protein database. The number of identified spectra with the homologous database was about half of that with the Escherichia coli K12 MG1655 database. We also tested TopPIC on a top-down mass spectrometry data set of human MCF-7 cells and obtained similar results.

conclusionsExperimental results demonstrated that TopPIC is capable of identifying many proteoform spectrum matches and localizing unknown alterations using homologous protein sequences containing no more than 2 mutations.

Indexed as

Sequence Homology, Amino AcidAmino Acid SequenceDatabases, ProteinEscherichia coliHumansMCF-7 CellsProteinsProteomeSoftwareTandem Mass SpectrometryProteinsProteomeHomologous protein databaseMass spectrometryTop-down

Identifiers

PMID30591035
PMCPMC6309053

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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.