Table 2.
Resource | Acronym | URL | Procedures/ Standards |
Human Protein Data | Proteomic Methodologies |
Reference |
---|---|---|---|---|---|---|
Chorus Project | https://chorusproject.org | n/a | User/experiment specific Cloud based platform for storage, analysis, and sharing of mass spectrometry data |
Mass Spectrometry | [106] | |
Human Kidney & Urine Proteome Project | HKUPP | www.hkupp.org alos accessible from www.hupo.org | Urine exosome collection and processing | Glomerulus Renal medulla Urine-normal Urine-exosome |
2-D Gel Electrophoresis CE-MS LC-MS/MS SELDI-TOF MS |
[69,100] |
Human Proteinpedia and Human Protein Reference Database | HPRD |
http://www.humanproteinpedia.org/ http://www.hprd.org/ |
n/a | Portal for sharing/integrating proteomic data | Mass Spectrometry Immunohistochemistry Immunofluorescence Western blotting Co-Immunoprecipitation Protein/Peptide microarray Yeast two hybrid screens |
[70] |
Human Proteome Organization | HUPO | www.hupo.org | Data interpretation guidelines | Links to multiple proteomic initiatives | Mass Spectrometry, antibodies, and the Knowledge Base | [159] |
Human Protein Atlas | HPA | http://www.proteinatlas.org/ | n/a | High-resolution images showing the spatial distribution of proteins in tissues | Immunohistochemistry Immunofluorescence RNASeq |
[5,93,156,160,164] |
Human Urine Database v3.0 | http://mosaiques-diagnostics.de/diapatpcms/mosaiquescms/front_content.php?idcat=257 | n/a | 25,000 peptides from independent samples for urine specimens from normal and diseased patients | CE-MS | [162] | |
Kidney & Urinary Pathway Knowledge Base | KUPKB | http://www.kupkb.org/#tab0 | n/a | Information extracted from scientific publications and other related renal databases using Semantic Web search tools | Multiple proteomics data from published literature | [157] (note new URL after publication) |
Max-Planck Unified Proteome Database | MAPU 2.0 | http://www.mapuproteome.com/urine/ | n/a | Protein sequences, function, motifs, references, & links to tissue sources and peptides | LTQ-FT and LTQ-Orbitrap mass spectrometer data | [67] |
PeptideAtlas | www.peptideatlas.org/hupo/hkup | n/a | Data repository for annotation of eukaryotic genomes via validation of expressed proteins | Mass Spectrometry | [42,71] | |
ProteomeXchange | http://www.proteomexchange.org/ | n/a | Provide a harmonized submission of MS proteomics data to the main existing repositories, and encourage data distribution | Shotgun mass spectrometry data sets | [163] | |
Sys-Body Fluid Database | http://www.biosino.org/bodyfluid/ | n/a | 11 body fluid databases compiled from scientific literature | Multiple data types | [158] | |
Urinary Exosomes Protein Database | https://hpcwebapps.cit.nih.gov/ESBL/Database/Exosome/ | n/a | Urinary exosomes protein database with GO annotations | Mass Spectrometry | [68,69] | |
UniProt | UniProt | http://www.uniprot.org/ | n/a | Unified view of protein sequence and functional information | Multiple data types | [165] |
Urine Proteomics | Urineproteomics.org | n/a | Links to methods, databases, companies and organizations | Mass Spectrometry | [42,114] | |
Yale Protein Expression Database | YPED | http://yped.med.yale.edu/repository/Welcome.do;jsessionid=ECB816BF54EE909E9FFDC1F7A70F2551 | n/a | Public access data repository | LCMS, MudPIT, ICAT, iTRAQ, SILAC, 2D Gel and DIGE, Progenesis and Skyline Label Free Quantitation, MRM analysis and SWATH | [89,161] |