PXD024236-1

PXD024236 is an original dataset announced via ProteomeXchange.

Title	Semi-automated positive pressure FASP in 96-well format (PF96) enables highly reproducible and time-efficient proteomics sample preparation of larger cohorts
Description	As novel technologies allow for a substantial increase in the number of LC-MS run per day, proteomics sample preparation appears as new bottle-neck for throughput. To overcome this limitation, we introduce a novel strategy for positive pressure 96-well filter-aided sample preparation (PF96) on a commercial positive pressure solid-phase extraction unit allowing for a 5-fold reduction in lab-time. Similar as conventional FASP, PF96 allows for robust processing of protein amounts between 3 and 60 µg, with higher analyte recovery observed for higher protein loads (36-60 µg). Notably, even lower amounts can be processed reproducibly, but at the expense of loss of peptide signal intensity (~40 % of signal intensity for 3 µg compared to 60 µg ) - more pronounced for peptides of higher retention time (reversed phase) and higher share of the hydrophobic amino acids F, L, M, W. Processing of 40 technical replicates of mouse heart tissue lysate highlights its reproducibility with Pearson Product-Moment correlations of r=0.9992 and r=0.9891 on protein and peptide level, respectively, which is similar to the reproducibility of LC-MS for replicate injections of identical samples.
HostingRepository	PRIDE
AnnounceDate	2021-12-03
AnnouncementXML	Submission_2021-12-03_04:57:54.348.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD024236
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Stefan Loroch
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	iodoacetamide derivatized residue
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2021-02-18 06:02:56	ID requested
⏵ 1	2021-12-03 04:57:54	announced

Dataset with its publication pending

submitter keyword: proteomics, sample preparation, automation, 96-well format

Albert Sickmann
contact affiliation	Leibniz-Institut für Analytische Wissenschaften – ISAS – e.V. Bunsen-Kirchhoff-Straße 11, 44139 Dortmund, Germany
contact email	sickmann@isas.de
lab head
Stefan Loroch
contact affiliation	Leibniz-Institut für Analytische Wissenschaften, Otto-Hahn-Straße 6b, 44227 Dortmund
contact email	stefan.loroch@isas.de
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD024236
     1. Label: PRIDE project
     2. Name: Semi-automated positive pressure FASP in 96-well format (PF96) enables highly reproducible and time-efficient proteomics sample preparation of larger cohorts