Q-Exactive Plus Orbitrap Mass Spectrometer (Thermo Fisher) 

 

How do global protein expression profiles or protein modification profiles change? What proteins interact with my protein of interest? Is this the protein I want?

Applications: 

  • Untargeted proteomics: identification and quantification of thousands of proteins isolated from complex biological matrices. Quantification can be performed using label free, absolute (e.g. SILAC) or multiplexed (e.g. TMT- or isobaric tags) workflows. 
  • Untargeted phosphoproteomics: identification and quantification of phosphorylated proteins.  
  • Affinity-purification mass-spectrometry (AP-MS): identification of protein-protein interactions in vivo using a combination of traditional immunoprecipitation/affinity purification and mass spectrometry analysis. Workflows using with and without cross-linking reagents are available.   
  • De novo protein and peptide sequencing: peptide and protein sequencing of protein/peptide samples purified on SDS-polyacrylamide, native, or blue-native polyacrylamide gels.  
Our Q-Exactive Orbitrap is used for a wide range of proteomics analysis including global proteomic and phosphoproteomic analysis, affinity-purification (AP-MS) experiments, and de novo protein sequencing. Coupled to a Dinoex UltiMate 3000 U-HPLC system, our nano-LC platform affords maximal sensitivity in peptide detection and identification, whether you are analyzing complex protein mixtures isolated from cells, tissues, and other biological matrices or less complex samples such as recombinant proteins, in-gel digested samples, or native protein samples. The high mass resolution of all ions in combination with indicative MS/MS fragments ensures sensitive and accurate detection while fast scanning at both a wide m/z range and a high mass resolution enables the detection and relative quantification of hundreds to thousands of peptides. 

 

How long does it take?  

A typical untargeted proteomics LC-MS/MS run usually takes ~140-160 mins to complete. This  ensures ample LC-separation of the thousands of peptides; for less complex samples, we generally use gradients of ~60 min. Data is largely acquired in data-dependent acquisition mode. In between each sample, a clean blank LC-MS/MS run is performed. These shorter (~45-60 min) runs ensure most residual peptides are “cleaned” from the column prior to the next sample injection. However, the LC-MS/MS times provided here are only estimates. Sample quantity and quality, MS methods, and other parameters may increase or decrease these times. Quality control samples, including digested lysate standards and peptide standards to assess for retention time accuracy and drift, are injected throughout samples batch runs as well as at the beginning and end of every to monitor instrument performance. All QC and clean blank data associated with their LC-MS/MS runs are provided to users.