PXD072920-1

PXD072920 is an original dataset announced via ProteomeXchange.

Title	Centrifugal microfluidic automation of the protein aggregation capture workflow for robust mass spectrometry-based proteomics
Description	Proteomic sample preparation for liquid chromatography-tandem mass spectrometry (LC-MS/MS) is increasingly addressed by automated approaches. However, in clinical settings, where only a limited amount of samples has to be processed in a standardized and reproducible manner, no fully automized workflow was provided yet. remains a major bottleneck for the broader adoption of clinical and translational proteomics due to its labor-intensive and error-prone nature. Here, we present the AutoPAC-Disk, a centrifugal microfluidic implementation of a protein aggregation capture (PAC) sample preparation workflow for bottom-up proteomics. The AutoPAC-Disk features a bead-packed column with a miniaturized digestion volume of 14 µL and pre-stored organic solvents. A comparative evaluation using HEK293 cell lysates revealed higher identification rates than both a manual commonly used reference workflow and a its semi-automated robotic system implementation (KingFisher), yielding 50 % and 37 % more peptide identifications and 23 % and 10 % more protein identifications, respectively. These gains in peptide identifications translated into increased sequence coverage of the identified proteins. Quantitative reproducibility was high for all approaches, with medianOur AutoPAC-Disk resulted in a similar exhibits high quantitative reproducibility with protein group intensity coefficients of variation below 10 %, similar to the other well -established workflows. Further analysis revealed that the AutoPAC-Disk predominantly enabled additional protein identifications in the low-abundance range. Together, these results provide a proof of concept that microfluidic automation, including the successful on-disk pre-storage of reagents and buffers, can substantially simplify proteomic sample preparation by enabling a high degree of automation and minimal user interaction. This approach lowers the operational barrier for personnel with limited experience in proteomic sample preparation and represents a promising strategy for future applications in clinical and translational proteomics within the field of precision medicine.
HostingRepository	PRIDE
AnnounceDate	2026-06-29
AnnouncementXML	Submission_2026-06-29_12:13:51.835.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Johanna Wallner
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606;
ModificationList	iodoacetamide derivatized residue
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2026-01-11 23:17:42	ID requested
⏵ 1	2026-06-29 12:13:52	announced

10.1039/D6LC00211K;

submitter keyword: proteomics, centrifugal microfluidics, personalized medicine,nLC-MS/MS, sample preparation, automation

Hannes Hahne
contact affiliation	OmicScouts, a Momentum Biotechnologies Company
contact email	hhahne@momentum.bio
lab head
Johanna Wallner
contact affiliation	Technical University of Munich
contact email	johanna.wallner@tum.de
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD072920
     1. Label: PRIDE project
     2. Name: Centrifugal microfluidic automation of the protein aggregation capture workflow for robust mass spectrometry-based proteomics