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GPMDB specifications


Unique identifier OMICS_02457
Alternative name Global Proteome Machine and Database
Restrictions to use None
Maintained Yes

Publications for Global Proteome Machine and Database

GPMDB citations


The Gene Centric Content Management System and Its Application for Cognitive Proteomics

PMCID: 5874771
PMID: 29473895
DOI: 10.3390/proteomes6010012

[…] ementation of C-HPP, the work of the proteome inventory was split among different teams and countries [].At the beginning of the C-HPP there were established resources on proteomic MS-data (PRIDE [], GPMdb [] and PeptideAtlas []); affinity data (Human Protein Atlas []); human proteome data in neXtProt []; and flexible platforms to work with heterogeneous molecular data, such as TAVERNA []. Despite […]


Myocilin Regulates Metalloprotease 2 Activity Through Interaction With TIMP3

PMCID: 5644706
PMID: 29049729
DOI: 10.1167/iovs.16-20336

[…] dification of methionine oxidation, and expectation value scores of 0.01 or lower. MGF files were searched using X!Hunter against the latest library available on the Global Proteome Machine Database (GPMDB) at the time. Other searches used the cRAP contaminant library from the GPMDB and libraries constructed from the latest Ensembl release available at the time. MGF files were searched using X!!Ta […]


Enhanced Missing Proteins Detection in NCI60 Cell Lines Using an Integrative Search Engine Approach

J Proteome Res
PMCID: 5737412
PMID: 28960077
DOI: 10.1021/acs.jproteome.7b00388
call_split See protocol

[…] requency in proteomic experiments were the input data. Tryptic peptides were obtained from neXtProt database using Proteogest software, and detection frequencies for each peptide were downloaded from GPMDB database ( The total number of observations for each peptide was defined considering all the observations independently of the parent ion charg […]


A Golden Age for Working with Public Proteomics Data

Trends Biochem Sci
PMCID: 5414595
PMID: 28118949
DOI: 10.1016/j.tibs.2017.01.001

[…] bility of reliable and more user-friendly resources and tools to support data sharing on the other hand , .The first MS proteomics resources were set up more than 10 years ago, notably PeptideAtlas , GPMDB , and PRIDE (now renamed PRIDE Archive) , , and these continue to be leading resources worldwide. Through the years, other proteomics resources have appeared and, regrettably, also disappeared . […]


Improvement of peptide identification with considering the abundance of mRNA and peptide

BMC Bioinformatics
PMCID: 5311845
PMID: 28201984
DOI: 10.1186/s12859-017-1491-5

[…] -Seq derived database with filtering proteins at low transcript abundance. In previous study, Shanmugam et al. found that the sensitivity of protein identification could improved by using RNA-Seq and GPMDB protein observation frequency. In their study, the probability adjustment of identification was limited at protein level but not for peptide, and the potential novel sequences from RNA-Seq data […]


Identifying the missing proteins in human proteome by biological language model

BMC Syst Biol
PMCID: 5259966
PMID: 28155671
DOI: 10.1186/s12918-016-0352-6

[…] ns contains 25 members []. The baseline metrics for the HPP contains five annually updated data resources []: the Ensembl database [] provides the possible genes coding proteins; Peptide Atlas [] and GPMdb [] separately screen high confident proteins from mass spectrometry data; the Human Protein Atlas [] is in charge of extracting proteins by antibody-based research; and finally neXtProt [] colle […]


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GPMDB institution(s)
Department of Biochemistry and Molecular Pharmacology, New York University Langone Medical Center, New York, NY, USA; Department of Biochemistry and Medical Genetics, The University of Manitoba, Winnipeg, MB, Canada

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