Useful Links and Resources - Seyfried Lab

Useful Links

Laboratory Space:

The Proteomics Core Lab is located in the Whitehead Biomedical Research Building, Room 525. It is entirely outfitted for cutting- edge protein analytical services via microcapillary liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) for highly sensitive protein identification, posttranslational site mapping, and protein quantification. Numerous computational tools have also been developed for high through data processing. Consultations are available for experimental design, data interpretation and grant application.

Lab Equipment:

Orbitrap Fusion Mass Spectrometer with Electron Transfer Dissociation (Thermo Scientific)

The fusion is an Orbitrap hybrid mass spectrometer is coupled to a UltiMate 3000 RSLCnano system. The Fusion is equipped with a mass filter, a collision cell, a high-field Orbitrap analyzer, and, finally, a dual cell linear ion trap analyzer (Q-OT-qIT). This system offers high MS/MS acquisition speed of 20 Hz and detects up to 19 peptides sequences within a single second of operation. The Fusion also has resolution in excess of 450,000 allowing for separation of isobaric interferences. The Emory Fusion is also equipped with Electron Transfer Dissociation (ETD), which is an orthogonal fragmentation technique to HCD and collision induced dissociation (CID) which will enhance peptide identification and localization of labile post-translational modifications (PTMs), such as glycosylation and phosphorylation.

Orbitrap Fusion Mass Spectrometer (Thermo Scientific)

Q-Exactive Plus Mass Spectrometer (Thermo Scientific)

The "Q-Exactive Plus" Orbitrap is coupled to nanoAcquity UPLC system. This instrument features high ion currents because of an S-lens, and fast high-energy collision-induced dissociation (HCD) peptide fragmentation because of parallel filling and detection modes. The e image current from the detector is processed by an .enhanced Fourier Transformation. algorithm, enabling high mass spectrometric resolution (up to 140,000 fwhm). With almost instantaneous isolation and fragmentation, the instrument can sequence 10 peptides per a second. This instrument is also capable of proteomics approach termed parallel reaction monitoring (PRM), which is a targeted proteomics strategy wherein all product ions of a peptide are simultaneously co-detected under conditions that offer high resolution and high mass accuracy.

LTQ Orbitrap Hybrid Mass Spectrometer (Thermo Scientific)

The LTQ Orbitrap mass spectrometer is coupled with an autosampler and HPLC system. The system allows automated capillary LC-MS/MS runs for top-down, middle-down and bottom-up analyses with high resolution (up to 100,000). It is capable of detecting peptides at subfemtomolar level, identifying hundreds to thousands of proteins in complex mixtures, mapping posttranslational modification sites, and quantifying proteins based on label-free methods or isotope labeling strategies (e.g. iTRAQ and SILAC).

Sorcerer IDA, Linux Beowolf with Sequest Cluster, Proteome Discoverer, Mascot, and Maxquant

The computational platform is capable of performing sophisticated data analyses, including database search (i.e. matching MS/MS spectra to peptide sequences), data filtering (i.e. removing false positive matches), statistical inference, as well as data storage, presentation and distribution.