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Protocols

cRAP specifications

Information


Unique identifier OMICS_25833
Name cRAP
Alternative name common Repository of Adventitious Proteins
Restrictions to use None
Community driven No
Data access File download
User data submission Not allowed
Maintained Yes

cRAP citations

 (31)
call_split

Intrinsically disordered N termini in human parechovirus 1 capsid proteins bind encapsidated RNA

2018
Sci Rep
PMCID: 5895611
PMID: 29643409
DOI: 10.1038/s41598-018-23552-7
call_split See protocol

[…] used searchGUI and the peptide sequences were compiled with peptideshaker,. Databases were created using HPeV1 protein sequences appended to a FASTA file containing the uniprot human proteome and the common repository of adventitious proteins database. Linear ion trap data was searched using a 0.3 Da mass error, and Orbitrap using 10 ppm error. Peptides appearing in the negative controls were used […]

library_books

Elucidation of cross species proteomic effects in human and hominin bone proteome identification through a bioinformatics experiment

2018
BMC Evol Biol
PMCID: 5819086
PMID: 29463217
DOI: 10.1186/s12862-018-1141-1

[…] on of semitryptic and non-tryptic peptides, which are a common feature of ancient proteome datasets [, ].A protein list containing commonly identified contaminants, composed of proteins listed on the common Repository of Adventitious Proteins and those mentioned in reference [], was added to each reference proteome (see Additional file ). No further modifications were made to the databases downloa […]

library_books

Homeolog expression analysis in an allotriploid non model crop via integration of transcriptomics and proteomics

2018
Sci Rep
PMCID: 5777989
PMID: 29358676
DOI: 10.1038/s41598-018-19684-5

[…] BAM files per cultivar (mpileup, SAMTools,), followed by variant calling, in reference to the Musa reference genome v2 (45,855 sequences) (bcftools, SAMTools),. Each database was complemented by 116 common repository of adventitious proteins (CRAP, http://www.thegpm.org/crap/) and combined into a target/decoy database enabling False Discovery Rate (FDR) estimation. The decoy sequences were create […]

library_books

Salmonella enterica Serovar Typhimurium Alters the Extracellular Proteome of Macrophages and Leads to the Production of Proinflammatory Exosomes

2018
Infect Immun
PMCID: 5778363
PMID: 29158431
DOI: 10.1128/IAI.00386-17

[…] Tandem mass spectrometry (MS/MS) samples were analyzed by using the SEQUEST algorithm (v1.3.0.339; Thermo Fisher). The protein database used for data bank searching contained common contaminants (the common Repository of Adventitious Proteins [cRAP]), Salmonella enterica serovar Typhimurium proteins, and human proteins (UniProt; total of 87,396 entries) assuming trypsin as the digestion enzyme. SE […]

library_books

Characterization of Trichuris muris secreted proteins and extracellular vesicles provides new insights into host–parasite communication

2018
J Extracell Vesicles
PMCID: 5795766
PMID: 29410780
DOI: 10.1080/20013078.2018.1428004

[…] t ion. Analyst 1.6.1 (ABSCIEX, Framingham, MA, USA) software was used for data acquisition and analysis.For the analysis of the ES products, a database was built using the T. muris genome [] with the common repository of adventitious proteins (cRAP, http://www.thegpm.org/crap/) appended to it. A similar database containing the T. muris genome, the cRAP and the Mus musculus genome was used for the […]

library_books

Proteomics Reveals the Molecular Underpinnings of Stronger Learning and Memory in Eastern Compared to Western Bees*

2017
PMCID: 5795390
PMID: 29187519
DOI: 10.1074/mcp.RA117.000159

[…] formatics Solutions Inc. Waterloo, Canada) was performed by searching against the sequence database (21,780 protein sequences of Apis mellifera, downloaded in February 2015 from NCBI), coupled with a common repository of adventitious proteins database (cRAP, downloaded from The Global Proteome Machine Organization, April, 2012). The search parameters were: parent ion tolerance, 15 ppm; fragment to […]

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