PXD025089-2

PXD025089 is an original dataset announced via ProteomeXchange.

Title	Towards zero variance in proteomics - positive pressure FASP in 96-well format (PF96) enables highly reproducible and time-efficient analysis of sample cohorts
Description	As 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.
HostingRepository	PanoramaPublic
AnnounceDate	2022-03-24
AnnouncementXML	Submission_2022-03-24_20:20:39.802.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Roman Sakson
SpeciesList	scientific name: Mus musculus; NCBI TaxID: 10090;
ModificationList	Carbamidomethyl; Label:13C(6)15N(2); Label:13C(6)15N(4)
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2021-03-29 18:56:12	ID requested
1	2021-11-24 07:20:17	announced
⏵ 2	2022-03-24 20:20:40	announced	: Added publication

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]

submitter keyword: automation, FASP, PF96, proteomics, sample preparation

Albert Sickmann
contact affiliation	ISAS e.V.
contact email	albert.sickmann@isas.de
lab head
Roman Sakson
contact affiliation	ISAS e.V.
contact email	roman.sakson@isas.de
dataset submitter

Panorama Public dataset URI