Oct 22, 2025
Sample Desalting and Clean-up using Agilent OMIX C18 TIPS for LC-MS/MS
- Katja Piltti1,
- Clinton Yu1
- 1University of California, Irvine
External link: https://doi.org/10.1038/s41467-025-66185-x
Protocol Citation: Katja Piltti, Clinton Yu 2025. Sample Desalting and Clean-up using Agilent OMIX C18 TIPS for LC-MS/MS. protocols.io https://dx.doi.org/10.17504/protocols.io.rm7vz92bxgx1/v1
Manuscript citation:
Piltti, K.M., Lakatos, A., Benavente-Perez, F. et al. C1q drives neural stem cell quiescence by regulating cell cycle and metabolism through BAI1. Nat Commun 16, 11386 (2025). https://doi.org/10.1038/s41467-025-66185-x
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: October 08, 2025
Last Modified: October 22, 2025
Protocol Integer ID: 229374
Keywords: Sample desalting, Sample clean-up, Peptide desalting, LC-MS/MS preparation, Proteomics sample prep, OMIX C18 tips, Protein digestion cleanup, Proteomic workflows, ms compatible with omix c18 pipette tip, bead digestion for lc, omix c18 tip, c18 tips for lc, omix c18 pipette tip, protein complexes for unbiased forward screen, sample digestion detail, ms compatible, bead digestion, using nanolc, lc, sample desalting, m, protein complex,
Funders Acknowledgements:
Wings for Life
Grant ID: WFL-US-01/18
Abstract
Compatible with OMIX C18 pipette tips, 10 - 100 μL (Agilent, Cat# A57003100). Sample digestion details are available in the "Denaturing On-bead Digestion for LC-MS/MS" –protocol. Step-by-step instructions for the pull-down are available in "Co-Immunoprecipitation/Pull-Down of C1q-Interacting Intracellular Proteins/Protein Complexes for Unbiased Forward Screen Using NanoLC-MS/MS"-protocol.
Materials
OMIX C18 pipette tips, 10 - 100 μL (Agilent, Cat# A57003100)
Required Buffers:
1. 100% Acetonitrile (ACN) (Sigma-Aldrich, Cat# A998-4)
2. 0.1% Formic acid (FA) (Fisher Scientific, Cat# 60-006-17)
3. 50% ACN, 0.1% FA
4. 90% ACN, 0.1% FA
Troubleshooting
Before start
*Sample digestion details are available in the Denaturing On-bead-Digestion for LC-MS/MS – protocol.
Pretreatment, Conditioning, and Equilibration of the Tips
Aspirate 100 μL of 100 % Acetonitrile (ACN) (Sigma-Aldrich, Cat# A998-4) and discard the solvent — repeat (Total 2x).
Aspirate 100 μL of 0.1% Formic acid (FA) (Fisher Scientific, Cat# 60-006-17) and discard solvent — repeat (Total 3x).
Sample Application
Aspirate 100 μL pre-treated sample* acidified to 0.1% FA into Equilibrated OMIX Tip.
*See the "Denaturing On-bead Digestion for LC-MS/MS" – protocol for details.
Dispense and aspirate the sample for 9 cycles (Total 10x).
Sample Washing
Aspirate 100 μL of 0.1% FA buffer and discard solvent — repeat (Total 2x).
Sample Elution
Aspirate 100 μL of (50% ACN, 0.1% FA)-buffer.
Dispense and aspirate the sample for 9 cycles (Total 10x).
Aspirate 100 μL of (90% ACN, 0.1% FA)-buffer.
Dispense and aspirate the sample for 9 cycles (total 10x).
Combine the eluent with the (50% ACN, 0.1% FA)-eluent, resulting in a final eluent concentration of 70% ACN, 0.1% FA. Concentrate the sample using a SpeedVac before LC-MS/MS.