Protein Identification

Protein identification is most commonly accomplished by proteolytic digestion followed by LC-MS/MS analysis.  After an in-depth project discussion, the sample is prepared by the user following our advised protocols, and submitted to the facility for analysis. Samples are enzymatically digested, run on nano-capillary HPLC/MSMS, and the MSMS spectra are correlated against a specific database for peptide identification.  If sending us a pulldown then we strongly prefer that you would elute your protein by acidic solution of 0.2 M Glycine pH3. Spin down beads, take buffer to another Eppendorf and neutralize to pH 7.5-8 and send it to us on dry ice, we will start from there.

Complex Mixture Analysis

Complex mixtures of proteins are identified by a number of single- and multi-dimensional approaches.  For example, MUDPit (Multidimensional Protein Identification Technology) starts with a solution digestion of the sample, then separation via ERLIC (electrostatic repulsion hydrophilic interaction chromatography) HPLC followed by reversed phase chromatography (RPLC).  For simple samples we can perform GeLC, in which an entire lane of an SDS-PAGE gel is excised into sections, affords the user a two dimensional separation of the protein mixture based on protein intact molecular weight (SDS-PAGE) and then individual peptide hydrophobicity by reversed phase chromatography (RPLC).

Posttranslational Modification Site Determination

Starting with a single highly purified protein in an SDS-PAGE gel slice, multiple sites of modification, eg. phosphorylation, acetylation and others, can be determined. This process involves a detailed project discussion and careful selection of multiple enzymes to maximize peptide coverage for specific sites of interest.

Quantitative Proteomics

One of the major challenges in modern proteomics is characterizing the differences in protein expression between two or more samples in a statistically relevant method. For instance, these methods could show differences in protein expression between treated and non-treated cell lines, healthy and sick animals, or between knockout and wild type organisms.

 Labeled: Quantitative mass spectrometry normally utilizes stable isotope labeling at the whole cell level, intact protein level or even peptide level. There are several well established techniques to do this, and a detailed project consultation prior to beginning an experiment with this goal is mandatory.

  •  SILAC (stable isotope labeling with amino acids in cell culture) is a simple and straightforward approach for in vivo incorporation of a label into proteins for mass spectrometry (MS)-based quantitative proteomics. SILAC relies on metabolic incorporation of a given ‘‘light’’ or ‘‘heavy’’ form of the amino acid into the proteins. The method relies on the incorporation of amino acids with substituted stable isotopic nuclei (e.g. deuterium, 13C, 15N). Thus in an experiment, two cell populations are grown in culture media that are identical except that one of them contains a ‘light’ and the other a ‘heavy’ form of a particular amino acid (e.g. 12C and 13C labeled L-lysine, respectively). When the labeled analog of an amino acid is supplied to cells in culture instead of the natural amino acid, it is incorporated into all newly synthesized proteins. After a number of cell divisions, each instance of this particular amino acid will be replaced by its isotope labeled analog. Since there is hardly any chemical difference between the labeled amino acid and the natural amino acid isotopes, the cells behave exactly like the control cell population grown in the presence of normal amino acid. It is efficient and reproducible as the incorporation of the isotope label is 100%, however is generally applicable only to cell or tissue culture experiments due in large part to the expense of stable isotope labeled growth media.
  • TMT (tandem mass tags) Isobaric chemical tags are powerful tools that enable concurrent identification and quantitation of proteins in different samples using tandem mass spectrometry. They are small chemical molecules with identical structure that covalently attach to the free amino termini of lysine residues of peptides and proteins, thereby labeling various peptides in a given sample. During the MS/MS analysis, each isobaric tag produces a unique reporter ion signature that makes quantitation possible. In a typical MS analysis, the labeled peptides are indistinguishable from each other; however, in the tandem MS mode during which peptides are isolated and fragmented, each tag generates a unique reporter ion. Protein quantitation is then accomplished by comparing the intensities of the six reporter ions in the MS/MS spectra.
  • Di-Methyl labelling analysis - uses stable isotope incorporation at the peptide level using fairly  inexpensive reagents and is applicable to most samples..
  • iTRAQ (Isotope Tags for Relative and Absolute Quantitation) is another popular technique that includes up to 10 isotopic labels for multiplexing experimental variables. The technique is based upon chemically tagging the N-terminus of peptides generated from protein. The labeled samples are then combined (post labeling), fractionated by nano-LC and analyzed by tandem mass spectrometry. Peptides are chromatographically resolved as single peaks with identical full MS masses. Fragmentation of the labeled peptides generates a low molecular mass reporter ion that is unique to the tag used to label each of the samples. Measurement of the intensity of these reporter ions, enables relative quantification of the peptides in each digest and hence the proteins from where they originate. This process has the advantage of no chromatographic interference from the labels but requires a low mass MSMS scan to observe the reporter ions.
  • AQUA – method of absolute quantitation based on synthetic "heavy" peptides that is used as an absolute standard. A fundamental goal of cell biology is to define the absolute levels of every protein expressed by an organism under the conditions of interest. Precise measurement of protein changes in terms of molecules per cell, and for all expressed components, would provide the high quality datasets necessary for a comprehensive understanding of disease at the molecular level. Absolute quantification of proteins uses 13C- and 15N- labeled synthetic reference peptides and tandem MS to measure expression in terms of number of molecules per cell. This process targets specific peptides individually and can become expensive but provides the most exact quantitation in many cases. Typically a SIM or SRM experiment is preformed on the mass spectrometer to target only the peptides of interest, so the method can be adapted to high throughput proteomics experiments.

 Label-free methods for quantitation have recently become popular and shown good results in blind studies that have been published. These processes rely on highly reproducible chromatography; typically with high pressure sub-2 micron particle reverse phase columns and traps, to produce statistically relevant data. The Thermo Fusion Lumos is one system that targets this type of analysis directly, with the Protein Expression System and nano-Acquity UPLC. This system eliminates the isolation step of MSMS data acquisition, relying on post-run analysis to construct individual MSMS spectra from the mix of MSMS data. Data is analyzed on either Maxquant or Proteome Discoverer 2.1

 C-terminal Sequence Analysis

In this lab, we use multiple enzymes to obtain redundant peptides which exhaustively define the C-terminal region of a purified protein. Multiple instrument runs are combined with custom bioinformatics tools to provide the final result.

Analysis of mammalian plasmas with depletion of IgG and Albumin protocol

Quantitative analysis of plasma proteomes after a depletion for IgG and Albumin protocol

Crosslinking experiments

Please call to discuss any of the above and we will be happy to work with you on these projects