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PXD025089

PXD025089 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleTowards zero variance in proteomics - positive pressure FASP in 96-well format (PF96) enables highly reproducible and time-efficient analysis of sample cohorts
DescriptionAs novel LC-MS technologies for proteomics offer substantial increase in LC-MS runs per day, robust and reproducible sample preparation emerges as a new bottleneck for throughput. We introduce a novel strategy for positive pressure 96-well filter-aided sample preparation (PF96) on a commercial positive pressure solid-phase extraction device. PF96 allows for a 5-fold increase in throughput in conjunction with extraordinary reproducibility on protein level (Pearson Product-Moment correlations of r=0.9993), as demonstrated for mouse heart tissue lysate in 40 technical replicates. Subsequent targeted quantification of 16 endogenous peptides in presence of stable-isotope-labeled reference peptides confirmed that PF96 variance is barely accessible against the technical variation originating from nanoLC-MS instrumentation. We further demonstrate that protein loads of 36-60 µg result in optimal peptide recovery, but also that lower amounts ≥ 3 µg can be reproducibly processed. In summary, reproducibility, simplicity and economy of time render PF96 a promising future for various applications in the field of proteomics including clinical and biomedical research.
HostingRepositoryPanoramaPublic
AnnounceDate2022-03-24
AnnouncementXMLSubmission_2022-03-24_20:20:39.802.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportSupported dataset by repository
PrimarySubmitterRoman Sakson
SpeciesList scientific name: Mus musculus; NCBI TaxID: 10090;
ModificationListCarbamidomethyl; Label:13C(6)15N(2); Label:13C(6)15N(4)
InstrumentQ Exactive HF
Dataset History
RevisionDatetimeStatusChangeLog Entry
02021-03-29 18:56:12ID requested
12021-11-24 07:20:17announced
22022-03-24 20:20:40announced: Added publication
Publication List
Loroch S, Kopczynski D, Schneider AC, Schumbrutzki C, Feldmann I, Panagiotidis E, Reinders Y, Sakson R, Solari FA, Vening A, Swieringa F, Heemskerk JWM, Grandoch M, Dandekar T, Sickmann A, Toward Zero Variance in Proteomics Sample Preparation: Positive-Pressure FASP in 96-Well Format (PF96) Enables Highly Reproducible, Time- and Cost-Efficient Analysis of Sample Cohorts. J Proteome Res, 21(4):1181-1188(2022) [pubmed]
Keyword List
submitter keyword: automation, FASP, PF96, proteomics, sample preparation
Contact List
Albert Sickmann
contact affiliationISAS e.V.
contact emailalbert.sickmann@isas.de
lab head
Roman Sakson
contact affiliationISAS e.V.
contact emailroman.sakson@isas.de
dataset submitter
Full Dataset Link List
Panorama Public dataset URI