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Zabell A.P.R.,Indigo Biosystems | Foxworthy T.,Indigo Biosystems | Eaton K.N.,Andor Labs | Julian R.K.,Indigo Biosystems
Journal of Chromatography A | Year: 2014

Typical area calculation for a chromatographic peak assumes the observed signal strength at every measurement is an exactly accurate count of the signal. We compared that approach to one using the exponentially modified Gaussian (EMG) in an automated, clinical production setting. Peak areas in a 47 analyte high throughput clinical production liquid chromatography-tandem mass spectrometry assay were compared across four months of production data to determine trends over the lifespan of a chromatographic column. The EMG parameters were superior to traditional quality control methods for monitoring data reproducibility, accuracy and precision. Because the EMG calculations are performed for every peak in the system, a constant monitor of system health is integrated into the operational workflow. Parameter trends confirmed the need for column replacement, and indicated the opportunity for a reduced schedule of preventive and routine maintenance. © 2014 Elsevier B.V.


Jones A.R.,University of Liverpool | Eisenacher M.,Ruhr University Bochum | Mayer G.,Ruhr University Bochum | Kohlbacher O.,University of Tübingen | And 16 more authors.
Molecular and Cellular Proteomics | Year: 2012

We report the release of mzIdentML, an exchange standard for peptide and protein identification data, designed by the Proteomics Standards Initiative. The format was developed by the Proteomics Standards Initiative in collaboration with instrument and software vendors, and the developers of the major open-source projects in proteomics. Software implementations have been developed to enable conversion from most popular proprietary and open-source formats, and mzIdentML will soon be supported by the major public repositories. These developments enable proteomics scientists to start working with the standard for exchanging and publishing data sets in support of publications and they provide a stable platform for bioinformatics groups and commercial software vendors to work with a single file format for identification data. © 2012 by The American Society for Biochemistry and Molecular Biology, Inc.


Mayer G.,Ruhr University Bochum | Jones A.R.,University of Liverpool | Binz P.-A.,Swiss Institute of Bioinformatics | Deutsch E.W.,Institute for Systems Biology | And 10 more authors.
Biochimica et Biophysica Acta - Proteins and Proteomics | Year: 2014

This paper focuses on the use of controlled vocabularies (CVs) and ontologies especially in the area of proteomics, primarily related to the work of the Proteomics Standards Initiative (PSI). It describes the relevant proteomics standard formats and the ontologies used within them. Software and tools for working with these ontology files are also discussed. The article also examines the "mapping files" used to ensure correct controlled vocabulary terms that are placed within PSI standards and the fulfillment of the MIAPE (Minimum Information about a Proteomics Experiment) requirements. This article is part of a Special Issue entitled: Computational Proteomics in the Post-Identification Era. Guest Editors: Martin Eisenacher and Christian Stephan. © 2013 Elsevier B.V.


Trademark
Indigo Biosystems | Date: 2012-01-06

computer software for automated chromatographic analysis and review.


Trademark
Indigo Biosystems | Date: 2012-01-06

Computer software for the management, acquisition, organization and retrieval and analysis of data and information, and delivery of such data and information through a real time dashboard.


Indigo Biosystems | Entity website

Working at Indigo. Indigo BioAutomation is a community of passionate and skilled individuals working together to change an industry ...


Indigo Biosystems | Entity website

Software. Everywhere ...


PubMed | Indigo Biosystems
Type: Journal Article | Journal: Bioanalysis | Year: 2010

This article describes the need for incurred sample reanalysis and suggests that the combination of a Bland-Altman plot and tolerance intervals can provide a visual evaluation of method performance. It also shows how the proposed combination is a tool that may be of value in determining minimum sample size. An example dataset is worked through in its entirety so that a reader unfamiliar with the topic can gain sufficient information to analyze their own data. Related topics include the generation of 66.7% tolerance factors, comparison of mean-normalized and log differences and the use of probability plots to evaluate error distributions. The suggestions presented in this article are meant to be a continuation of the ongoing incurred sample reanalysis discussion and, as such, further comment is invited.


Indigo Biosystems | Entity website

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