PXD025089-1

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	2021-11-24
AnnouncementXML	Submission_2021-11-24_07:20:16.716.xml
DigitalObjectIdentifier
ReviewLevel	Non 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

Dataset with its publication pending

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