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1.  The Gel Electrophoresis Markup Language (GelML) from the Proteomics Standards Initiative 
Proteomics  2010;10(17):3073-3081.
The Human Proteome Organisation’s Proteomics Standards Initiative (HUPO-PSI) has developed the GelML data exchange format for representing gel electrophoresis experiments performed in proteomics investigations. The format closely follows the reporting guidelines for gel electrophoresis, which are part of the Minimum Information About a Proteomics Experiment (MIAPE) set of modules. GelML supports the capture of metadata (such as experimental protocols) and data (such as gel images) resulting from gel electrophoresis so that laboratories can be compliant with the MIAPE Gel Electrophoresis guidelines, while allowing such data sets to be exchanged or downloaded from public repositories. The format is sufficiently flexible to capture data from a broad range of experimental processes, and complements other PSI formats for mass spectrometry data and the results of protein and peptide identifications to capture entire gel-based proteome workflows. GelML has resulted from the open standardisation process of PSI consisting of both public consultation and anonymous review of the specifications.
doi:10.1002/pmic.201000120
PMCID: PMC3193076  PMID: 20677327
data standard; gel electrophoresis; database; ontology
2.  Identification of Diagnostic Urinary Biomarkers for Acute Kidney Injury 
Acute kidney injury (AKI) is an important cause of death among hospitalized patients. The two most common causes of AKI are acute tubular necrosis (ATN) and prerenal azotemia (PRA). Appropriate diagnosis of the disease is important but often difficult. We analyzed urine proteins by 2-DE from 38 patients with AKI. Patients were randomly assigned to a training set, an internal test set or an external validation set. Spot abundances were analyzed by artificial neural networks (ANN) to identify biomarkers which differentiate between ATN and PRA. When the trained neural network algorithm was tested against the training data it identified the diagnosis for 16/18 patients in the training set and all 10 patients in the internal test set. The accuracy was validated in the novel external set of patients where 9/10 subjects were correctly diagnosed including 5/5 with ATN and 4/5 with PRA. Plasma retinol binding protein (PRBP) was identified in one spot and a fragment of albumin and PRBP in the other. These proteins are candidate markers for diagnostic assays of AKI.
doi:10.231/JIM.0b013e3181d473e7
PMCID: PMC2864920  PMID: 20224435
Acute kidney injury; Biomarkers; Diagnosis; Kidney; Urine

Results 1-2 (2)