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Core Facility — Proteomic Mass Spectrometry
In-gel Digestion Protocol
click here to download the paper In-gel digestion for mass spectrometric characterization of proteins and proteomes
click here to download the in-house protocol for the in-gel digestion for mass spectrometric characterization of proteins and proteomes
click here to download the in-house protocol for high reducing environment in-gel digestion (8M urea)
click here to download the in-house protocol for filter aided sample preparation in high reducing environment in-gel digestion (FASP urea/ SP3; If you needed to use detergents during your experiment)
click here to download the in-house protocol for high reducing environment in-gel digestion (8M urea)
click here to download the in-house protocol for filter aided sample preparation in high reducing environment in-gel digestion (FASP urea/ SP3; If you needed to use detergents during your experiment)
SP3 - single-pot, solid-phase-enhanced sample-preparation
Molecular Systems Biologynature protocols
Sera-Mag SpeedBeads and Sera-Mag Carboxylate-Modified Magnetic Particles
In order to obtain a systems-level understanding of a complex biological system, detailed proteome information is essential. Despite great progress in proteomics technologies, thorough interrogation of the proteome from quantity-limited biological samples is hampered by inefficiencies during processing. To address these challenges, here we introduce a novel protocol using paramagnetic beads, termed Single-Pot Solid-Phase-enhanced Sample Preparation (SP3). SP3 provides a rapid and unbiased means of proteomic sample preparation in a single tube that facilitates ultrasensitive
analysis by outperforming existing protocols in terms of efficiency, scalability, speed, throughput, and flexibility SP3 provides a simplified platform for processing of protein samples before MS-based proteomics analysis.
SP2: Rapid and Automatable Contaminant Removal from Peptide Samples for Proteomic Analyses
J. Proteome Res.Sera-Mag SpeedBeads and Sera-Mag Carboxylate-Modified Magnetic Particles
Peptide cleanup is essential for the removal of contaminating substances that may be introduced during sample preparation steps in bottom-up proteomic workflows. The benefits of carboxylate-modified paramagnetic particles over traditional reversed-phase methods for detergent and polymer removal let us implement this approach into CF-PMS for already digested samples with unknown contaminants. We are using this easy-to-use standard operating protocol, termed SP2, which can be applied to remove detergents and polymers from peptide samples while concentrating the sample in solvent that is directly compatible with our LC–MS workflows. The authors demonstrate that SP2 can be applied to phosphopeptides and glycopeptides.
S-Trap
Protifi
The patent-pending S-Trap brings universal, simple and inexpensive sample preparation to bottom-up proteomics. One easy-to-use spin column combines sample concentration, clean up and digestion. S-Trap sample processing does not require any specialized equipment nor training. From µg to mg scales, your samples are ready in about an hour. S-Traps eliminate one of the greatest sources of variability – inconsistent lysis and protein solubilization – by using strong 5% SDS for all samples. This almost universal protein solvent is removed in the protein trap of the S-Trap, which retains all undigested proteins but does not retain small molecules including the SDS used to extract and handle proteins.
MS-safe Affinity Purification
click here to download the paper Global landscape of HIV–human protein complexes
click here to download the Supplementary Data of
click here to download the Excel-sheet IP protocol