PXD001695

PXD001695 is an original dataset announced via ProteomeXchange.

Title	A double-barrel LC-MS/MS system to quantify 96 interactomes per day
Description	The field of proteomics has evolved hand-in-hand with technological advances in LC-MS/MS systems, now enabling the analysis of very deep proteomes in a reasonable time. However, most applications do not deal with full cell or tissue proteomes, but rather with restricted sub-proteomes relevant for the research context at hand or resulting from extensive fractionation. At the same time, investigation of many conditions or perturbations puts a strain on measurement capacity. Here we develop a high throughput workflow capable of dealing with large numbers of low or medium complexity samples and specifically aim at the analysis of 96-well plates in a single day (15 min per sample). We combine parallel sample processing with a modified liquid chromatography platform driving two analytical columns in tandem, which are coupled to a quadrupole Orbitrap mass spectrometer (Q Exactive HF). The modified LC platform eliminates idle-time between measurements and the very high sequencing speed of the Q Exactive HF dramatically reduces required measurement time. We apply the pipeline to the yeast chromatin remodeling landscape, and demonstrate quantification of 96 pull-downs of chromatin complexes in about one day. This is achieved with only 500 µg input material, enabling yeast cultivation in a 96-well format. Our system retrieved known complex-members and the high throughput allowed probing with many bait proteins. Even alternative complex compositions were detectable in these very short gradients. Thus, sample throughput, sensitivity and LC/MS-MS duty cycle are improved several-fold compared to established workflows. The pipeline can be extended to different types of interaction studies and to other medium complexity proteomes.
HostingRepository	PRIDE
AnnounceDate	2015-05-07
AnnouncementXML	Submission_2015-05-07_08:07:15.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Mario Oroshi
SpeciesList	scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationList	No PTMs are included in the dataset
Instrument	LTQ Orbitrap; Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2015-01-19 05:27:19	ID requested
⏵ 1	2015-05-07 08:07:17	announced

Hosp F, Scheltema RA, Eberl HC, Kulak NA, Keilhauer EC, Mayr K, Mann M, A Double-Barrel Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS) System to Quantify 96 Interactomes per Day. Mol Cell Proteomics, 14(7):2030-41(2015) [pubmed]

curator keyword: Technical

submitter keyword: Saccharomyces cerevisiae

interactomics

chromatography

method development

high throughput analysis

Matthias Mann
contact affiliation	Department of Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany
contact email	mmann@biochem.mpg.de
lab head
Mario Oroshi
contact affiliation	Proteomics
contact email	oroshi@biochem.mpg.de
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/2015/05/PXD001695

PRIDE project URI

• PRIDE
  1. PXD001695
     1. Label: PRIDE project
     2. Name: A double-barrel LC-MS/MS system to quantify 96 interactomes per day