The entire complement of proteins, protein-protein interactions and post-translational modifications within an organism is known as its proteome; the moniker being a blend of protein and genome. Since protein modifications, such as phosphorylation, acetylation, glycosylation and methylation, are state-dependent, the proteome is constantly changing in response to cellular cues. Proteome-focused studies, then, must specify the conditions under which the proteome was analyzed. Proteomics is the study of the proteome. Like genomics, proteomics is a branch of bioanalysis that provides valuable data about a cell. Unlike genomics, in which data can be gathered from any cell of an organism, proteomics relies on cell specific, temporal and environment specific readouts.
Modern proteomics benefits from the ability to assess the modification state of proteins directly, using a combination of techniques such as mass spectrometry, western blotting and enrichment. The proteome of a cell is of much greater complexity than the genome.
Proteomics includes these areas of focus:
FAQs for Proteomics
- I am using Trypsin and am wondering about specificity. Does it cut at additional sites when in high concentration?
- Which residues does Endoproteinase AspN cut?
- What is the Proteinase K activity in commonly used buffers?
- I have a very low concentration of protein and would prefer not to denature as a separate step with buffer exchange before digestion. What denaturants can he use in the Trypsin reaction itself?
- How does one do a Trypsin in-gel digest?
- Is there a simple way to remove Trypsin after protein cleavage?
- Are there any amino acid residues that inhibit or reduce the efficiency of digestion of glutamate residues in a peptide sequence with Endoproteinase GluC? The site I want to digest has a glutamate residue followed by a proline residue and some enzymes are inhibited by the presence of a proline after the hydrolysis site.
Protocols for Proteomics
- O-Glycosidase (P0733)
- O-Glycosidase Application Note 1 (P0733)
- a1-2,4,6 Fucosidase O Digestion of Released Labeled Glycans Protocol
- Cleavage of the Fusion Protein Generated Using The pMAL Protein Fusion and Purification System (E8200)
- Cloning a PCR Fragment Into a pMAL Expression Vector (E8200)
- Endo D Removal Magnetic Chitin Bead Protocol (P0742)
- Endo F2 Reaction Protocol (P0772)
- Endo H/Endo Hf Protocol
- Endo S Removal Magnetic Chitin Bead Protocol (P0741)
- Endo-α-N-Acetylgalactosaminidase Application Note 1
- Glycoproteomics: Buffer Exchange Protocols (P0711)
- In-gel Digestion Protocol for Endoproteinase LysC (P8109)
- PNGase F Protocol
- Purification of a Fusion Protein generated by The pMAL Protein Fusion and Purification System (E8200)
- Quick Start Guide (E8200)
- Rapid PNGase F (non-reducing format) (P0711) Reaction Protocol
- Rapid PNGase F (non-reducing format) (P0711) SDS-PAGE Protocol
- Reaction Conditions for Endo D (P0742)
- Reaction Conditions for Endo S (P0741)
- Reaction Conditions for IdeZ Protease (IgG-specific) (P0770)
- Reaction Conditions for PNGase A (P0707)
- Reaction Conditions for Remove-iT® PNGase F (P0706)
- Reaction conditions for Simultaneous Digestion of IgG with IdeZ Protease (IgG-specific) and PNGase F (fragmentation and deglycosylation) (P0770)
- Reaction Protocols for Protein Deglycosylation Mix (P6039)
- Removal of Endo F2 by Magnetic Beads (P0772)
- Removal of terminal N-acetylglucosamine from the biantennary N-linked sugars of IgG
- Remove-iT® PNGase F Magnetic Chitin Bead Protocol (P0706)
- RNase B Deglycosylation Protocol (P7817)
- Separating the Protein of Interest from MBP after Protease Cleavage Using The pMAL Protein Fusion and Purification System (E8200)
- Typical Reaction Conditions (P0732)
- Typical Reaction Conditions for Endo F3 Protocol (P0771)
- Typical Reaction Conditions for Endoproteinase LysC
- Typical Reaction Conditions for α1-2, 3, 4, 6 Fucosidase (P0748)
- Typical Reaction Conditions for α1-3, 4 Fucosidase (P0769)
- Typical Reaction Conditions for α1-3, 4, 6 Galactosidase (P0747)
- Typical Reaction Conditions for α2-3 Neuraminidase (P0728)
- Typical Reaction Conditions for α2-3,6,8 Neuraminidase (P0720)
- Typical Reaction Conditions for α2-3,6,8,9 Neuraminidase A (P0722)
- Typical Reaction Conditions for β1-4 Galactosidase (P0730)
- Western Transfer Protocol for Anti-MBP Monoclonal Antibody
The Glycoproteomics brochure provides information on the suite of endo- and exoglycosidases, and deglycosylation enzymes offered by NEB.
Glycoproteomics Technical Guide
Find in-depth information, including protocols, technical tips, frequently asked questions and application notes, utilizing NEB’s suite of endo- and exoglycosidases.
Rapid PNGase F Trifold
Learn how Rapid PNGase F can speed up your antibody deglycosylation step and make your therapeutic proteins faster and more efficiently than ever before.