Widening the Proteolysis Bottleneck: A New Protein Sample Preparation Tool

The poster featured in this blog provides background information and data on development of Rapid Digestion-Trypsin.

The poster featured in this blog provides background information and data on development of Rapid Digestion-Trypsin.

Improvements in Protein Bioprocessing

As more and more protein-based therapeutics enter research pipelines, more efficient protocols are needed for characterization of protein structure and function, as well as means of quantitation. One main step in this pipeline, proteolysis of these proteins into peptides, presents a bottleneck and can require optimization of multiple steps including reduction, alkylation and digestion time.

We have developed a new trypsin reagent, Rapid Digestion–Trypsin, that streamlines the protein sample preparation process, reducing the time to achieve proteolysis to about 1 hour, a remarkable improvement over existing overnight sample preparation times.

How Does it Work?

With this new trypsin product, proteolysis is performed at 70°C, incorporating both denaturation and rapid digestion. The protocol can be used with multiple protein types, including pure proteins and complex mixtures, and is compatible with digestion under native, reduced or nonreduced conditions.

Continue reading

ProteaseMAX: A Surfactant for the Most Complex Mixtures

Alternate Proteases CoverHere we provide two examples of “atypical” experiments that take advantage of the properties of the ProteaseMAX™ Surfactant to improve studies involving digestion of complex protein mixtures.

Example 1
Clostridium difficile spores are considered the morphotype of infection, transmission and persistence of C. difficile infections. A recent publication (1) illustrated a novel strategy using three different approaches  to identify proteins of the exosporium layer of C. difficile spores and complements previous proteomic studies on the entire C. difficile spores. Continue reading

Filter-Aided Sample Preparation before Mass Spec Analysis: An Evaluation of FASP and eFASP

12271ma_800pxFilter-aided sample preparation (FASP) method is used for the on-filter digestion of proteins prior to mass-spectrometry-based analyses (1,2). FASP was designed for the removal of detergents, and chaotropes that were used for sample preparation. In addition, FASP removes components such as salts, nucleic acids and lipids. Akylation of reduced cysteine residues is also carried out on filter, after which protein is proteolyzed by use of trypsin on filter in the optimal buffer of the enzyme. Subsequent elution and desalting of the peptide-rich solution then provides a sample ready for LC–MS/MS analysis.

Erde et al. (3) described an enhanced FASP (eFASP) workflow that included 0.2% DCA in the exchange, alkylation, and digestion buffers,thus enhancing trypsin proteolysis, resulting in increases cytosolic and membrane protein representation. DCA has been reported (4) to improve the efficiency of the denaturation, solubilization, and tryptic digestion of proteins, particularly proteolytically resistant myoglobin and integral membrane proteins, thereby enhancing the efficiency of their identification with regard to the number of identified proteins and unique peptides.

In a recent publication (5) traditional FASP and eFASP were re-evaluated by ultra-high-performance liquid chromatography coupled to a quadrupole mass filter Orbitrap analyzer (Q Exactive). The results indicate that at the protein level, both methods extracted essentially the same number of hydrophobic transmembrane containing proteins as well as proteins associated with the cytoplasm or the cytoplasmic and outer membranes.

The LC–MS/MS results indicate that FASP and eFASP showed no significant differences at the protein level. However, because of the slight differences in selectivity at the physicochemical level of peptides, these methods can be seen to be somewhat complementary for analyses of complex peptide mixtures.

  1. Manza, L. L. et al. (2005) Sample preparation and digestion for proteomic analyses using spin filters Proteomics  5, 1742–74.
  2. Wiśniewski, J. R. et al. (2009) Universal sample preparation method for proteome analysis Nat. Methods 6, 359–62.
  3. Erde, J. et al. (2014) Enhanced FASP (eFASP) to increase proteomic coverage and sample recovery for quantitative proteome experiments. J. Proteome Res. 13, 1885–95.
  4. Lin, Y. et al. (2008) Sodium-deoxycholate-assisted tryptic digestion and identification of proteolytically resistant proteins Anal. Biochem.  377, 259–66.
  5. Nel. A. et al. (2015) Comparative Reevaluation of FASP and Enhanced FASP methods by LC-MS/MS/ J Proteome Res. 14, 1637–42.

Optimizing Trypsin Digestion Parameters for Plasma Proteins

TrypsinLysC Page 2Biomarkers in biological fluids in particular have the potential to inform regarding risk of disease or to allow early detection for more effective treatment. Plasma/serum is considered the universal source of biomarkers. This fluid is, indeed, easily collected, and the important point is that plasma collects proteins from each and every tissue, compared to other fluids such as urine or cerebrospinal fluid. Optimizing experimental conditions (i.e., use of trypsin for the digestion of target proteins) used to discover or monitor biomarkers in plasma is critical to successful detection of biomarkers.

In a recent publication by Proc et al., plasma denaturation/digestion protocols were compared using quanititation methods. In this reference 14 combinations of heat, solvent (acetonitrile, methanol, trifluoroethanol), chaotropic agents (guanidine hydrochloride, urea) and surfactants (sodium dodecyl sulfate (SDS)and sodium deoxycholate (DOC) with effectiveness in improving tryptic digestion. Digestion efficiency was monitored by quantitating the peptides from 45 moderate- to high-abundance plasma proteins using tandem mass spectrometry in multiple reaction mode with a mixture of stable isotope labeled analogues of these peptides as internal standards. In the results, Proc et al. noted that use of either DOC and SDS produced an increase in the overall yield of tryptic peptides. Since SDS is not compatible with mass spectrometry and DOC can be easily remove by acid precipitation, the overall recommendation was the use of DOC with a nine hour digestion procedure.

Literature Cited:

Proc, J.L. et al. (2010) A Quantitative Study of the Effects of Chaotropic  Agents Surfactants and Solvents on the Digestion Efficiency of Human Plasma Proteins by Trypsin J. Proteome Res. 9, 5422–37.

Asp-N Protease: Applications Update

TrypsinLysC Page 2

Asp-N, Sequencing Grade, is an endoproteinase that hydrolyzes peptide bonds on the N-terminal side of aspartic and cysteic acid residues: Asp and Cys. Asp-N activity is optimal in the pH range of 4.0–9.0. This sequencing grade enzyme can be used alone or in combination with trypsin or other proteases to produce protein digests for peptide mapping applications or protein identification by peptide mass fingerprinting or MS/MS spectral matching. It is suitable for  in-solution or in-gel digestion reactions.

The following references illustrate the use of Asp-N in recent publications:

Protein sequence coverage

  1. Jakobsson, M et al. (2013)  Identification and characterization of a novel Human Methyltransferase modulating Hsp70 protein function through lysine methylation. J. Biol. Chem. 288, 27752–63.
  2. Carroll, J. et. al. (2013) Post-translational modifications near the quinone binding site of mammalian complex I.  J. Biol. Chem. 288, 24799–08.

Glycoprotein analysis

  1. Siguier, B. et al. (2014) First structural insights into α-L-Arabinofuranosidases from the two GH62 Glycoside hydrolase subfamilies. J. Biol. Chem. 289, 5261–73.
  2. Vakhrushev, S. et al. (2013) Enhanced mass spectrometric mapping of the human GalNAc-type O-glycoproteome with SimpleCells. Mol. Cell. Prot. 12, 932–44.
  3. Berk, J. et al. (2013) . O-Linked β-N- Acetylglucosamine (O-GlcNAc) Regulates emerin binding to autointegration Factor (BAF) in a chromatin and Lamin B-enriched “Niche”.  J. Biol. Chem. 288, 30192–09.

Phosphoprotein analysis

  1. Roux, P. and Thibault, P. (2013) The Coming of Age of phosphoproteomics –from Large Data sets to Inference of protein Functions. Mol. Cell. Prot. 12, 3453–64.

Increased protein identification using Pseudomonas and Lysobacter Lys-C proteases

Alternate Proteases CoverOwing to efficient proteolysis and particular advantages of trypsin-generated peptides for mass spectrometry analysis, trypsin is the most widely used proteomic protease. Recently, however, Lys-C has been increasingly used as either a trypsin alternate or as supplement. Its increasing favor is largely due to its ability to perform proteolytic digestion under protein denaturing conditions, an attribute that can greatly extend the observable proteome.

Lys-C is found in number of bacterial hosts with Lysobacter enzymogenes being used as a most popular source of commercially available Lys-C. We have now developed a recombinant form of Lys-C from Pseudomonas aeruginosa. We have compared performance of Pseudomonas and Lysobacter Lys-C.
Surprisingly, we found difference between Pseudomonas and Lysobacter Lys-C proteases on peptide level. The peptides generated by the proteases had much smaller overlap (25%) than typically observed between runs for the same sample indicating different bias toward lysine cleavage sites for Pseudomonas and Lysobacter Lys-C.
The proteases might have different proteolytic mechanisms. In fact, difference in proteolytic mechanisms is not unexpected considering the limited homology between these two proteases
Therefore we recommend combined digestion with Pseudomonas and Lysobacter Lys-C to maximize peptide and protein identification.

For a detailed technical review of these two protease visit: http://www.promega.com/resources/scientific_posters/posters/a-novel-recombinant-lysc-protease-for-proteomic-sample-preparation-scientific-poster/

Trypsin/Lys-C Mix: Alternative for standard trypsin protein digestions

Trypsin/Lys-C Mix, Mass Spec Grade, is a mixture of Trypsin Gold, Mass Spectrometry Grade, and rLys-C, Mass Spec Grade. The Trypsin/Lys-C Mix is designed to improve digestion of proteins or protein mixtures in solution.It is a little known fact that trypsin cleaves at lysine residues with lesser efficiency than at arginine residues. Inefficient proteolysis at lysine residues is the major cause of missed (undigested) cleavages in trypsin digests.


Supplementing trypsin with Lys-C enables cleavage at lysines with excepetional efficiency and specificity. Following the conventional trypsin digestion protocol (i.e., overnight incubation at nondenaturing conditions, reduction,alkylation, 25:1 protein:protease ratio [w/w], mix and incubate overnight at 37°C.) Replacing trypsin with Trypsin/Lys-C Mix in this conventional protocol leads to multiple benefits for protein analysis including more accurate mass spectrometry-based protein quantitation and improved protein mass spectrometry analytical reproducibility.

ProteaseMAX Surfactant: Enhanced In-solution Digestion Applications

ProteaseMax 11228MAThe primary advantage of ProteaseMAX™ Surfactant is that it improves identification of proteins in gel by enhanced protein digestion, increased peptide extraction, and minimized post digestion peptide loss. However, ProteaseMAX™ Surfactant can also facilitate in-solution digestion protocols.

ProteaseMAX™ Surfactant offers two major benefits for digesting proteins in solution. Continue reading

Proteinase K: An Enzyme for Everyone

protein expression purification and analysisWe recently posted a blog about Proteinase K, a serine protease that exhibits broad cleavage activity produced by the fungus Tritirachium album Limber. It cleaves peptide bonds adjacent to the carboxylic group of aliphatic and aromatic amino acids and is useful for general digestion of protein in biological samples. In that previous blog we focused on its use to remove RNase and DNase activities. However, the stability of Proteinase K in urea and SDS and its ability to digest native proteins make it useful for a variety of applications. Here we provide a brief list of peer-reviewed citations that demonstrate the use of proteinase K in DNA and RNA purification, protein digestion in FFPE tissue samples, chromatin precipitation assays, and proteinase K protection assays: Continue reading

Use of Multiple Proteases for Improved Protein Digestion

ResearchBlogging.orgOne of the approaches to identify proteins by mass spectrometry includes the separation of proteins by gel electrophoresis or liquid chromatography. Subsequently the proteins are cleaved with sequence-specific endoproteases. Following digestion the generated peptides are investigated by determination of molecular masses or specific sequence. For protein identification the experimentally obtained masses/sequences are compared with theoretical masses/sequences compiled in various databases.

Trypsin is the favored enzyme for this application, for the following reasons: A) the peptides contain a basic residue (Arg or Lys) on the C terminus and thus are good candidates for collision induced activation (CAD) in tandem experiments (low charge states and high mass-to-charge ratios); B) it is relatively Inexpensive; and C) optimal digestion conditions have been well characterized.

An inherent limitation of trypsin is the size of the peptides that it generates. For most organisms > 50% of tryptic peptides are less than 6 amino acids, too small for mass spectrometry based sequencing.

One recent publication examined the use of multiple proteases (trypsin, LysC, ArgC , AspN and GluC) in combination with either CAD or electron-based fragmentation (ETD) to improve protein identification (1). Their results indicated a significant improvement from a single protease digestion (trypsin), which yielded 27,822 unique peptides corresponding to 3313 proteins. In contrast using a combination of proteases with either CAD or ETD fragmentation methods yielded 92,095 unique peptides mapping to 3908 proteins.

Swaney DL, Wenger CD, & Coon JJ (2010). Value of using multiple proteases for large-scale mass spectrometry-based proteomics. Journal of proteome research, 9 (3), 1323-9 PMID: 20113005