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PXD008535 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleMaxQuant Label Free Quantification wrapped as a Software Service
DescriptionScientific services in the area of OMICS research is becoming increasingly popular. In gen- eral omics research can produce a massive amount of data that can pose a challenge for computing infrastructure. While in the genomics area, many applications can run on Linux nodes the situation in proteomics is different. In proteomics, many applications are optimized to run on Windows computer only. As a sci- entific service provider, a core facility needs reliable, reproducible and easy to use integrated solutions. Liquid chromatography mass spectrometry intensity based label-free quantifica- tion using data-dependent acquisition is a popular approach in proteomics to perform relative quantification of proteins in complex samples. MaxQuant is a widely used software for this type of analysis which has a complex graphical user interface and provides information-rich outputs. We run it in which also includes Scaffold for search result validation and visualization and an R based quality control report generation. Data analysis workflows consists of several components: a workflow engine, compute hosts, and archives. In particular, applications can run on compute hosts, while the data is kept in an archive server. Therefore, the input and output need to be staged to the compute host and the results need to be staged back to the archive. This complexity can be overwhelming for a most common user. These different components have all been integrated into a robust and user-friendly application to process standardized label-free quantification experiments. We integrated MaxQuant as an in-house Software as a Service application so it can be used by any workflow engine in a platform-independent manner. In this manuscript, we provide a technical description of how MaxQuant as software service has been integrated into our heterogeneous compute environment for reproducible and automatic large scale high throughput data processing of label-free quantification experiments. In this Pride dataset we provide four raw files along with the full MaxQuant results, the Scaffold file, the QC-pdf report to have a concrete idea of the potential of our workflow. These data are generated in the FGCZ-course in Nov. 2016 (for further information see: http://www.fgcz.ch/education/genomics-courses01.html).
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterJonas Grossmann
SpeciesList scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationListmonohydroxylated residue; iodoacetamide derivatized residue; deamidated residue
InstrumentQ Exactive
Dataset History
RevisionDatetimeStatusChangeLog Entry
02017-12-21 08:01:14ID requested
12022-09-23 05:31:08announced
Publication List
Dataset with its publication pending
Keyword List
curator keyword: Technical
submitter keyword: Proteomics, Label Free Quantification, Software as a Service, Data Dependent Aquisition, MaxQuant, Quality Control, Scientific Workflows and Services, Automation, Reproducible Research
Contact List
Grossmann Jonas
contact affiliationFunctional Genomics Center Zurich Winterthurerstr. 190 CH-8057 Zurich, Switzerland
contact emailjg@fgcz.ethz.ch
lab head
Jonas Grossmann
contact affiliationFunctional Genomics Center Zurich (UZH/ETHZ)
contact emailjg@fgcz.ethz.ch
dataset submitter
Full Dataset Link List
Dataset FTP location
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PRIDE project URI
Repository Record List
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