Cell lysis is the first step when extracting proteins for mass spectrometry applications. Fractionation may be required to enrich for proteins of interest or to study protein localization. The kits featured here are convenient, easy to use, and have been validated for downstream analysis with Thermo Scientific mass spectrometers. They include options for either total protein extraction or isolation of proteins from specific cellular fractions. The Thermo Scientific EasyPep Mini MS Sample Prep Kit provides pre-formulated reagents and a robust method for the preparation of high quality samples that are ready for MS analysis in less than 3 hours.

  • Optimized—extract total protein or specific cellular fractions
  • Effective—enable high protein yields with low cross-contamination for fractionation kits
  • Validated—extract from cultured mammalian cells have been successfully analyzed using Thermo Scientific mass spectrometers
  • Convenient—minimize the need for mechanical cell disruption

Choose the right protein extraction kit for your mass spec workflow

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  Pierce™ Mass Spec Sample Prep Kit for Cultured Cells
Thermo Scientific EasyPep Mini MS Sample Prep Kit

Mem-PER Plus Membrane Protein Extraction Kit

Subcellular Protein Fractionation Kit
for Cultured Cells 
Fractions isolated Primarily cytosolic Integral and membrane-associated proteins Nucleus, cytoplasm, membrane, cytoskeletal, chromatin-bound
Amount of sample processed 20 samples of 10-100 µg of cell pellet or tissue 50 samples of
5 million cells each
50 samples of
2 million cells each
(20 µL packed)
Sample processing time (pre-digestion) <30 min 1 hr 2–3 hr
Digestion proteases included? Yes No No
Total sample preparation time 1.5-3.5 hr 24-48 hr 24-48 hr

Featured product data

Comparison of protein yields by four mass spec sample prep lysis methods.

Comparison of protein yields by four mass spec sample prep lysis methods. From one culture of HeLa S3 cells, duplicate pellets containing 2 x 106 cells were resuspended and lysed using 0.2 mL of the respective buffers and protocol of each method (all include a sonication step); then protein concentrations and yields were determined. FASP: 0.1 M Tris-HCl, 4% SDS, 0.1 M DTT, pH 7.6. AmBic-SDS: 0.05 M ammonium bicarbonate, 0.1% SDS, pH 8.0. Urea: 0.1 M Tris-HCl, 8 M urea, pH 8.5. Kit Buffer: Lysis buffer from the Pierce Mass Spec Sample Prep Kit for Cultured Cells (Cat. No. 84840).

Representative quantitation

Representative quantitation of protein enrichment of marker proteins (Hsp90 and histone 3) using TMTsixplex reagents in different subcellular fractions relative to whole cell lysate. The red bars show the relative intensity of TMT reagent reporter ions for unique marker proteins. Subcellular fractions were prepared using the Thermo Scientific Subcellular Protein Fractionation Kit for Cultured Cells (Cat. No. 78840).

Identification of peptides by LC-MS/MS from immunoprecipitated Na+/ K+-ATPase transport complex extracted with the Mem-PER Plus Kit (Cat. No. 89842). Samples were processed by in-solution digestion according to the kit protocol, and analyzed on the Orbitrap Fusion mass spectrometer.

Protein Peptide sequence Xcorr value
Na+/K+-transporting ATPase subunit beta-1 VAPPGLTQIPQIQK 2.67
Na+/K+-transporting ATPase subunit alpha-1 LSLDELHR 2.20