PXD008535-1

PXD008535 is an original dataset announced via ProteomeXchange.

Title	MaxQuant Label Free Quantification wrapped as a Software Service
Description	Scientific 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).
HostingRepository	PRIDE
AnnounceDate	2022-09-23
AnnouncementXML	Submission_2022-09-23_05:31:08.245.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Jonas Grossmann
SpeciesList	scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue; deamidated residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2017-12-21 08:01:14	ID requested
⏵ 1	2022-09-23 05:31:08	announced
2	2024-10-22 05:39:46	announced	2024-10-22: Updated project metadata.

Dataset with its publication pending

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

Grossmann Jonas
contact affiliation	Functional Genomics Center Zurich Winterthurerstr. 190 CH-8057 Zurich, Switzerland
contact email	jg@fgcz.ethz.ch
lab head
Jonas Grossmann
contact affiliation	Functional Genomics Center Zurich (UZH/ETHZ)
contact email	jg@fgcz.ethz.ch
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2022/09/PXD008535

PRIDE project URI

• PRIDE
  1. PXD008535
     1. Label: PRIDE project
     2. Name: MaxQuant Label Free Quantification wrapped as a Software Service