Dataset Information

CFdb: A harmonized resource of co-fractionation mass spectrometry data

ABSTRACT: A total of 411 co-fractionation mass spectrometry (CF-MS) experiments were downloaded from public proteomics repositories such as PRIDE and MassIVE, then re-analyzed with MaxQuant. This repository provides complete MaxQuant outputs from all 411 experiments.

INSTRUMENT(S): LTQ Orbitrap, LTQ Orbitrap Velos, LTQ, Q Exactive

ORGANISM(S): Rattus Norvegicus (rat) Caenorhabditis Elegans Oryza Sativa (rice) Xenopus Laevis (african Clawed Frog) Triticum Aestivum (wheat) Drosophila Melanogaster (fruit Fly) Homo Sapiens (human) Escherichia Coli Trypanosoma Brucei Arabidopsis Thaliana (mouse-ear Cress) Zea Mays (maize) Dictyostelium Discoideum (slime Mold) Mus Musculus (mouse)

SUBMITTER: Michael Skinnider

LAB HEAD: Leonard Foster

PROVIDER: PXD042664 | Pride | 2024-01-26

REPOSITORIES: Pride

ACCESS DATA

Publications

Mapping protein states and interactions across the tree of life with co-fractionation mass spectrometry.

Skinnider Michael A MA Akinlaja Mopelola O MO Foster Leonard J LJ

Nature communications 20231215 1

We present CFdb, a harmonized resource of interaction proteomics data from 411 co-fractionation mass spectrometry (CF-MS) datasets spanning 21,703 fractions. Meta-analysis of this resource charts protein abundance, phosphorylation, and interactions throughout the tree of life, including a reference map of the human interactome. We show how large-scale CF-MS data can enhance analyses of individual CF-MS datasets, and exemplify this strategy by mapping the honey bee interactome. ...[more]

PMID: 38102123

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Project 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).

Dataset Information

CFdb: A harmonized resource of co-fractionation mass spectrometry data

Publications

Mapping protein states and interactions across the tree of life with co-fractionation mass spectrometry.

Similar Datasets

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