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PXD014182 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleAn automated ‘cells-to-peptides’ sample preparation workflow for high-throughput, quantitative proteomic assays of microbes
DescriptionMass spectrometry–based quantitative proteomic analysis has proven valuable for clinical and biotechnology related research and development. Driving this value have been improvements in the sensitivity, resolution, and robustness of mass analyzers. However, manual sample preparation protocols are often a bottleneck for sample throughput and can lead to poor reproducibility, especially for applications where thousands of samples per month must be analyzed. To alleviate these issues, we developed a ‘cells-to-peptides’ automated workflow for Gram-negative bacteria and fungi that includes cell lysis, protein precipitation, resuspension, quantification, normalization, and tryptic digestion. The workflow takes two hours to process 96 samples from cell pellets to the initiation of the tryptic digestion step and can process 384 samples in parallel. We measured the efficiency of protein extraction from various amounts of cell biomass and optimized the process for standard liquid chromatography-mass spectrometry systems. The automated workflow was tested by preparing 96 E. coli samples and quantifying over 600 peptides that resulted in a median coefficient of variation of 15.8%. Similar technical variance was observed for three other organisms as measured by highly-multiplexed LC-SRM-MS acquisition methods. These results show that this automated sample preparation workflow provides robust, reproducible proteomic samples for high-throughput applications.
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportSupported dataset by repository
PrimarySubmitterChris Petzold
SpeciesList scientific name: Escherichia coli; NCBI TaxID: 562; scientific name: Pseudomonas putida KT2440; NCBI TaxID: 160488; scientific name: Saccharomyces cerevisiae; NCBI TaxID: 4932; scientific name: Rhodotorula toruloides; NCBI TaxID: 5286;
ModificationListDeamidated; Carbamidomethyl
Instrument6460 Triple Quadrupole LC/MS
Dataset History
RevisionDatetimeStatusChangeLog Entry
02019-06-07 15:30:34ID requested
12019-08-23 16:48:02announced
Publication List
Chen Y, Guenther JM, Gin JW, Chan LJG, Costello Z, Ogorzalek TL, Tran HM, Blake-Hedges JM, Keasling JD, Adams PD, García Martín H, Hillson NJ, Petzold CJ, Sample Preparation Workflow for High-Throughput, Quantitative Proteomic Assays of Microbes. J Proteome Res, 18(10):3752-3761(2019) [pubmed]
Keyword List
submitter keyword: Automation, Sample preparation, Proteomics, Bacteria, Fungi, Microbes, Biotechnology, High-throughput
Contact List
Chris Petzold
contact affiliationLawrence Berkeley National Laboratory
contact emailcjpetzold@lbl.gov
lab head
Chris Petzold
contact affiliationLawrence Berkeley National Laboratory
contact emailcjpetzold@lbl.gov
dataset submitter
Full Dataset Link List
Panorama Public dataset URI