Protein-works: Protein Profiling

MS Bioworks protein profiling services (MSB-05, 06, 07, 08) are used to provide a high quality catalogue of proteins present in a sample. The service can be used with or without fractionation, with the precondition that a greater number of fractions will provide a greater number of identified proteins and greater numbers of peptides per protein. The basic experimental workflow for this service is presented below.

For the line items described here protein level fractionation is performed using SDS-PAGE. Alternative fractionation strategies such as reverse phase, Hydrophilic Interaction Liquid Chromatography (HILIC), anion exchange, cation exchange and removal of abundant proteins are available upon request as part of our Custom-Works services.

Characterization of MCF10A cells

Service ID MSB-05 MSB-06 MSB-07 MSB-08
Number of fractions 0 10 20 40
No. of proteins (≥2 peptides/protein) 847 2989 4573 5913
No. of unique peptides 4539 29117 46788 68646
Total spectral count 6829 54549 95986 181654
Mean spectral count/protein 8.1 18.2 21 30.7
Median spectral count/protein 5 8 9 12
Mean unique peptides/protein 5.4 9.7 10.2 11.6
Median unique peptides/protein 4 6 6 7
Protein false discovery rate (%) 0.8 0 0.2 0.3
No. of proteins (≥2 peptides/protein) 847 2989 4573 5913
No. of proteins (≥3 peptides/protein) 688 2682 4134 5563


MSB-05, 06, 07, 08 can be ordered directly from our online ordering system, here.