Defining a New Standard for Rigorous Protein Identification
The Waters® IdentityE High Definition Proteomics™ system, which integrates nanoACQUITY UPLC® and Synapt HDMS™ or Q-Tof Premier™ technologies, is designed exclusively for authoritative and comprehensive qualitative analysis. Taking advantage of the superior resolution of UPLC separations and the novel approach of MSE, the IdentityE system provides outstanding chromatographic results and simultaneous precursor and product ion information. UPLC/MSE data is then combined with IdentityE informatics to catalog complex protein digest mixtures and deliver more peptides, more proteins, more coverage, and more statistical rigor than conventional LC/MS/MS methods.
“ONE HIT WONDERS” AND LIMITATIONS OF EXISTING PROTEIN ID METHODS
The established bottom-up LC/MS-based peptide and protein identification methods employed over the past decade focus on the degree of similarity between an experimentally-acquired tryptic peptide mass spectrum and theoretical peptide spectra predicted from data banks of known (or translated) protein sequences, with little regard to their chromatographic retention.
These traditional approaches consider each tryptic peptide in virtual isolation with limited reference to their biological context or structural significance, and with no consideration of their plausible detectability within a complex mixture. For plausible detection of any tryptic peptide, researchers must consider the dynamic range and sensitivity of the MS detector as well as the protein capacity of the LC column employed. The proteomics community frequently voices concerns about the validity of these “one hit wonders,” where protein identity is assigned on the evidence of a single peptide, matched on the basis of spectral similarity alone.
ANALYTICAL COMPLETENESS
The Waters IdentityE system conclusively identifies proteins matched with multiple peptides by paying full attention to each peptide’s chromatographic retention time, exact precursor and product ion masses, significance within a protein, biological context, and plausible detectability.
This system solution for proteomics begins with a kinetically-tuned protein digestion protocol to marginalize missed cleavages, followed by direct nanoflow UPLC separations that deliver unprecedented peak capacity and retention time repeatability. A unique high-resolution mass spectrometry configuration enables peptide detection with an unmatched combination of dynamic mass resolution and bandwidth to ensure consistent over-sampling of complex protein digests. Mining deeper into the UPLC/MSE data, the system delivers comprehensive and specific multi-peptide identifications over an extended dynamic range with peptide ion accounting informatics. Quality control standards, defined methods, training, and support ensure reproducible operation and consistent results.
The result – an analytically-complete approach to identify more peptides and proteins with greater sequence coverage and statistical rigor than conventional LC/MS/MS methods.
Please visit www.waters.com/identity for Waters IdentityE High Definition Proteomics system news and applications.
Further Information: http://www.waters.com/identity
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