Table 2.

Human kidney/bladder/urine proteome/peptidome resources for best practice guidelines, data repositories, and integrative knowledge databases.

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]