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available"],"repository":["GPMDB"],"pubmed_abstract":["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 subproteomes 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 high sequencing speed of the Q Exactive HF 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 1 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 severalfold compared with established workflows. The pipeline can be extended to different types of interaction studies and to other medium complexity proteomes."],"pubmed_title":["A Double-Barrel Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS) System to Quantify 96 Interactomes per Day."],"pubmed_authors":["Hosp Fabian F,Scheltema Richard A RA,Eberl H Christian HC,Kulak Nils A NA,Keilhauer Eva C EC,Mayr Korbinian K,Mann Matthias M,","Hosp Fabian F, Scheltema Richard A RA, Eberl H Christian HC, Kulak Nils A NA, Keilhauer Eva C EC, Mayr Korbinian K, Mann Matthias M"],"name_synonyms":["LC-MS2, liquid chromatography tandem mass spectroscopy, organ system, LC/MS/MS, anatomical systems, LCMSMS, liquid chromatography-tandem mass spectroscopy, body system., LC-MSMS, LC-MS/MS, liquid chromatography tandem mass spectrometry, system, connected anatomical system, LC-MS-MS"],"description_synonyms":["big, APR, data, cou, HSN1E, determination, mol, LRP, DNMT, nutrient medium, APOER, EA1, MCMT, MLR-3, Tl3, Tl2, Cell, BAF155, BL-AC/P26, large, Workflows, AIM, CD91, Lr, CRACC1, chemical analysis, TGFBR5, Low, Work Flow, early activation antigen CD69, CXXC9, early T-cell activation antigen p60, ADCADN, me75, SWI3, medium, cell, growth medium, activation inducer molecule, SRG3, NOXA, expanded, min, D17Mit170, T1, sample population, sample., leukocyte surface antigen Leu-23, A2MR, enlarged, GP32/28, great, LRP1A, Bra, C-type lectin domain family 2 member C, Rsc8, assay, CD69, Work Flows, CLEC2C, IGFBP3R"],"pubmed_title_synonyms":["LC-MS2, liquid chromatography tandem mass spectroscopy, organ system, LC/MS/MS, anatomical systems, LCMSMS, liquid chromatography-tandem mass spectroscopy, body system., LC-MSMS, LC-MS/MS, liquid chromatography tandem mass spectrometry, system, connected anatomical system, LC-MS-MS"],"pubmed_abstract_synonyms":["liquid chromatography tandem mass spectroscopy, big, forelimb autopodium, chromatin remodelling, Meth, Activity, determination, HSN1E, Effects, Laboratory, nutrient medium, EA1, baker's yeast, Gene, MLR-3, Chalk, body system, Saccharomyces italicus, Long Term, LC-MS-MS, CYCLE, period, organ field, large, AIM, Ccne, forelimb autopod, chromatin modeling, LC-MSMS, yeast, Tina, Gene Products, system, field, Low, Research Activity, Work Flow, early activation antigen CD69, Effect, Laboratory Research, sensitivity, Chromatins, lager beer yeast, Priorities, chromatin modelling, portion of tissue, study, me75, anatomical systems, LCMSMS, Glass, Longterm, Research, cell, activation inducer molecule, developmental field, HAND, Tissue, min, stubby, Saccharomyes cerevisiae, proteins, Long-Term, Saccharomyces uvarum var. melibiosus, ecotype, D17Mit170, T1, foot, hand, leukocyte surface antigen Leu-23, Candida robusta, Ice, Saccharomyces capensis, great, sample, chromosome scaffold, C-type lectin domain family 2 member C, Sensitivity, Long-Term Effect, Development and Research, Research Priority, brewer's yeast, Long-Term Effects, forefoot of quadruped, LC-MS2, cou, Proteins, LC-MS/MS, DNMT, Liquid Chromatography, Longterm Effect, Research Priorities, future organ, terminal segment of free upper limb, MCMT, Tl3, Tl2, Cell, Saccaromyces cerevisiae, strain, BL-AC/P26, Sccharomyces cerevisiae, polypeptide, shortened, LC/MS/MS, Workflows, Priority, Lr, paw, fore-paw, chemical analysis, Long Term Effects, Protein, Proteomes., Research Activities, tissue portion, simple tissue, cultivar, connected anatomical system, forefeet, Crystal, Research and Development, CXXC9, Saccharomyces oviformis, deep, early T-cell activation antigen p60, ADCADN, Yeast, medium, growth medium, expanded, Specificity, sample population, Longterm Effects, Hands, Activities, organ system, Protein Gene Products, Speed, Gene Proteins, enlarged, GP32/28, Specificity and Sensitivity, fore foot, liquid chromatography-tandem mass spectroscopy, velocity, hand region, Bra, fore paw, forepaw, liquid chromatography tandem mass spectrometry, assay, forefoot, short, Proteomes, time, CD69, Work Flows, 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File: 20140827_EXQ00_FaHo_SA_SWI3_03.mzml. Published as part of Mol Cell Proteomics. 2015 Apr 17  . From the Abstract: {{i}} ... 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) ... {{/i}}","dates":{"submission":"2015-05-09"},"accession":"GPM11210038526","cross_references":{"pubmed":["25887394"],"Pride":["PXD001695"],"pride":[],"Pride Archive":["PXD001695"]}}