74th ASMS Conference on Mass Spectrometry and Allied Topics
May 31 - June 4, 2026 | San Diego, California, USA
AFFINISEP BREAKFAST SEMINAR
High Throughput Sample Preparation Methods for MS-Based Proteomics
Tuesday, June 2, 2026 | 7:00 - 8:15 AM
Tuesday, June 2, 2026 | 7:00 - 8:15 AM
High Throughput Sample Preparation Methods for MS-Based Proteomics
This seminar will present innovative Affinisep SPE kits designed to streamline sample preparation in MS-based proteomics. After a quick overview of Affinisep's know-how for sample preparation in MS-based proteomics by Dr. Kaynoush Naraghi, we will have the pleasure of welcoming Dr. Brett S. Phinney, the Director of the UC Davis Proteomics Core Facility at the Genome Center.
He will present data comparing alternative tips (AttractSPEĀ® Disks Tips) for the Evosep One system against standard Evotips, offering a candid look at how core facilities can adapt to increasing sample volumes while maintaining scientific rigor.
For this work, Brett compared both types of C18 tips on the same Evosep / Bruker timsTOF HT system using 50 ng of standardized HeLa cell lysate analyzed by DIA at 100 samples per day. AttractSPEĀ® Disks Tips were run with three wash-solvent variants (ACN, IPA, and combined ACN+IPA, n=3 for each washing conditions), while the Evosep tips were run using their standard preparation protocol (n=3). Twelve injections in total were processed with DIA-NN.
The most striking observation was a systematic MS1-signal difference between the tip types: roughly a 20% lower MS1 signal for Evosep, and not traceable to any single bad injection. Identification yields tracked the same pattern, with ~7% increase in precursors identification and ~3% increase in proteins identification with AttractSPEĀ® Disks Tips. Intra-group median CVs were tight in all conditions (1.0ā2.7%), and Evosep showed the highest precursor-level missingness (22.4% vs. 14.5ā19.3% for the Affinisep washes).
At the proteome level, the Evosep ā Affinisep (combined wash) contrast returned 1,381 differentially expressed proteins at adj.P < 0.05 ā with a striking directional asymmetry: 1,357 proteins (~98%) were higher with the AttractSPEĀ® Disks Tips, and only 24 were higher in the Evosep tips. The proteins under-recovered by Evosep were enriched for secreted, extracellular, and membrane-associated species (NAMPT, GDF15, CGA, HTRA1, TIMP1, ITGA1/2, ITGB1, SERPINB3, C3), while the small set of proteins relatively elevated in Evosep was largely cytoskeletal (KRT1, TUBA1B, POTEI) ā consistent with relative-quantification mirror effects rather than genuine biological differences.
These are observations from a single experiment on one instrument. Additional tests and comparisons will be carried out soon and independent replication, orthogonal quantification, and ideally an external-lab swap will also be needed before drawing any definitive methodological conclusion.
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Affinisep develops and manufactures from A to Z high quality and ready-to-use microelution SPE kits to simplify sample preparation in proteomics, and help you achieve highly reliable results. Available with a wide range of formats and capacities Affinisepās kits are the ideal solutions for various applications and workflows, from few samples processed manually, to high throughput processing of hundreds of samples, and this applies to samples ranging from single-cell analysis to peptide quantities up to several mg.
SPEAKER INFORMATION
Dr. Kaynoush Naraghi
Dr. Kaynoush Naraghi is the CEO and co-founder of Affinisep, a life sciences company specializing in innovative sample preparation technologies. Holding a PhD in Polymer Chemistry, Kaynoush began her career in research and development before transitioning into executive leadership in 2004.
Kaynoush leads strategic R&D investments and oversees the development of advanced sample-preparation kits for proteomics, food quality control, and water analysis. These solutions are designed to enhance accuracy, efficiency, and reproducibility in complex analytical workflows, helping scientists and laboratories achieve more reliable results across a wide range of testing environments.
Dr. Brett Phinney
Dr. Brett S. Phinney is the Director of the UC Davis Proteomics Core Facility at the Genome Center, where he has led the facility since 2005. With over two decades of mass spectrometry expertise ā including prior leadership of the proteomics facility at Michigan State University ā Brett specializes in MS-based proteomics, biofluid profiling for biomarker identification, and quantitative protein analysis via LC-MS/MS. Under his leadership, the core has served more than 1,500 unique principal investigators across 643 institutions, processed nearly 9,000 projects. The facility currently operates a Bruker timsTOF HT, Thermo Orbitrap Fusion Lumos, and Thermo Orbitrap Exploris 480. Brett is also active in community education through online tutorials, Proteomics YouTube videos, an annual short course in proteomics, and proteomics software development.