# Yale University
**Source**: https://cbic.yale.edu/instruments-listing?field_instrument_type_value=Mass+Spectrometry
**Parent**: https://cbic.yale.edu/instruments
# Instrument Catalog
Instrument Type
- Any -Diffraction (X-ray and electron)ImagingMass SpectrometryNMR & EPROptical SpectroscopyScatteringSolution BiophysicsStructural Science
Instrument Location
- Any -CRB 100KCL 3KCL 7KCL 11KCL 12KCL 16BSCL 148SCL 136SCL 123SCL 123aSCL 26
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Instrument NameDate of AcquisitionInstrument Type
Order
AscDesc
GC-MS Agilent 6890N/5973
**Short Name:** GC-MS
**Instrument Type:** Mass Spectrometry
**Instrument Location:** KCL 3
**Date of Acquisition:** February 2004
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Open access GC-MS instrument with 100-position sample changer and 20 meter column installed.
[Standard Operating Procedure](https://cbic.yale.edu/sites/default/files/files/GCMS%20SOP.pdf)
GC-MS column selection
**Short Name:** GC-MS columns
**Instrument Type:** Mass Spectrometry
**Instrument Location:** KCL 3
**Date of Acquisition:** September 2021
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| | | | | | |
| --- | --- | --- | --- | --- | --- |
| **Column Name** | **Manufacturer** | **Thickness (um)** | **Length (m)** | **Diameter (mm)** | **Max. Temp. (deg C)** |
| SH-Rxi-5Sil MS | Shimadzu | 0.25 | 30 | 0.25 | 350 |
| DB select 624UI | Agilent | 1.4 | 30 | 0.25 | 260 |
| ZB-WAX | Zebron | 0.5 | 30 | 0.25 | 250 |
| PoraPLOT Q | Agilent | 8 | 25 | 0.25 | 250 |
| EC-1 | Grace | 0.25 | 30 | 0.25 | 350 |
| VF-WAXms | Agilent | 1 | 30 | 0.25 | 260 |
| Rtx-1 | Restek | 0.25 | 15 | 0.25 | 350 |
| Stabilwax-MS | Restek | 0.25 | 30 | 0.25 | 260 |
GC-TQ-MS Shimadzu 8050 NX
**Short Name:** GC-TQ-MS
**Instrument Type:** Mass Spectrometry
**Instrument Location:** KCL 3
**Date of Acquisition:** December 2019
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[**Shimadzu 8050 NX Triple Quadrupole (TQ) GC-MS**](https://www.ssi.shimadzu.com/products/gas-chromatography-mass-spectrometry/gcms-tq8050-nx.html) with Liquid Injection, Solid Phase Micro Extraction (SPME) and Headspace Analysis Autosampler. Triple Quadrupole MS instruments allow for quantitation of compounds, collision induced dissociation (CID) and multiple reaction monitoring (MRM). The system is equipped with an Electron Ionization (EI) source, a Chemical Ionization (CI) source and a Flame Ionization Detector (FID).
LC-MS Shimadzu 8060 TQ
**Short Name:** 8060
**Instrument Type:** Mass Spectrometry
**Instrument Location:** KCL 3
**Date of Acquisition:** January 2020
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Service only [**Shimadzu LCMS-8060**](https://www.ssi.shimadzu.com/products/liquid-chromatography-mass-spectrometry/lcms-8060.html) Triple Quadrupole Liquid Chromatograph Mass Spectrometer (LC-MS/MS). Triple Quadrupole MS instruments allow for quantitation of compounds, collision induced dissociation (CID) and multiple reaction monitoring (MRM) with high sensitivity. The UPLC system includs a fluidic system with two different solvents, three trays for up to 54 samples each (in GC vials), three UPLC columns (see list below) and a photo-diode array (UV/Vis) detector. 96 and 384 well plates can be used for screening projects, please reach out first.
Column 1: Shim-pack Scepter C18-120 1.9mum - 2.1 x 50mm\
Column 2: Shim-pack Scepter C18-120 1.9mum - 2.1 x 100mm\
Column 3: Shim-pack Scepter C8-120 1.9mum - 2.1 x 100mm
Different columns can be installed on demand.
Standard Solvents available for LC separation:
Water (with 0.1% Formic Acid or 10mM NH4Ac)\
Methanol (with and w/o 0.1% Formic Acid or 10mM NH4Ac)\
Acetonitrile (with and w/o 0.1% Formic Acid or 10mM NH4Ac)
Different solvents can be used on demand.
LC-MS Shimadzu 9030 Quadrupole Time-of-Flight MS
**Short Name:** 9030
**Instrument Type:** Mass Spectrometry
**Instrument Location:** KCL 3
**Date of Acquisition:** January 2020
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[**Shimadzu LCMS-9030**](https://www.ssi.shimadzu.com/products/liquid-chromatography-mass-spectrometry/lcms-9030.html) Quadrupole Time-of-Flight High-Performance Liquid Chromatograph Mass Spectrometer for high-resolution MS.
Service only high resolution Q-tof MS instrument with an UPLC system, including a fluidic system with two different solvents, three trays for up to 54 samples each (in GC vials), three UPLC columns (see list below) and a photo-diode array (UV/Vis) detector. 96 and 384 well plates can be used for screening projects, please reach out first.
Column 1: Shim-pack Scepter C18-120 1.9mum - 2.1 x 50mm\
Column 2: Shim-pack Scepter C18-120 1.9mum - 2.1 x 100mm\
Different columns can be installed on demand.
Standard Solvents available for LC separation:
- Water (with 0.1% Formic Acid or 10mM NH4Ac)
- Methanol (with and w/o 0.1% Formic Acid or 10mM NH4Ac)
- Acetonitrile (with and w/o 0.1% Formic Acid or 10mM NH4Ac)
Different solvents can be used on demand.
LC-MS ThermoScientific QExactive Orbitrap (+ IR spectroscopy)
**Short Name:** Orbi
**Instrument Type:** Mass Spectrometry
**Instrument Location:** KCL 3
**Date of Acquisition:** August 2019
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Service only high resolution **[QExactive Orbitrap FT-MS](https://planetorbitrap.com/q-exactive)** instrument with an Dionex 3000 UPLC system, including a fluidic system with up to four different solvents, three trays for up to 40 samples each (in 2 mL GC vials), one UPLC column, a UV/Vis photo-diode array (PDA) and a fluorescence (FL) detector.
The structural mass spectrometry extension on this instrument allows for recording of infrared spectra of mass selected ions in the gas phase. Read more about the technique .
Software for opening and converting .raw files: <http://msfragger.nesvilab.org/tutorial_convert.html>
LC-MS Waters Xevo Qtof high-resolution MS
**Short Name:** Xevo
**Instrument Type:** Mass Spectrometry
**Instrument Location:** KCL 3
**Date of Acquisition:** November 2018
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Service only high resolution Q-tof MS instrument with an UPLC system, including a fluidic system with up to four different solvents, two trays for up to 48 samples each (in GC vials), four UPLC columns (see list below) and a photo-diode array (UV/Vis).
Column 1: Acquity UPLC BEH C18 1.7mum - 2.1 x 50mm\
Column 2: Acquity UPLC BEH Glycan 1.7mum - 2.1 x 100mm\
Column 3: Acquity UPLC BEH300 C18 1.7mum - 2.1 x 100mm\
MALDI-ToF-MS Shimadzu AXIMA Confidence
**Short Name:** MALDI
**Instrument Type:** Mass Spectrometry
**Instrument Location:** KCL 3
**Date of Acquisition:** January 2020
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[AXIMA Confidence](https://www.ssi.shimadzu.com/products/maldi-tof-mass-spectrometry/axima-confidence.html) Linear/Reflectron MALDI-TOF Mass Spectrometer from Shimadzu.
**Target Plates available:**\
AXIMA 384 well (2.8mm I.D.) plate - P/N: DE1580TA
| | |
| --- | --- |
| *Number of wells:* | *Sample = 384 Calibrant = 0* |
| *Internal diameter of wells:* | *Sample = 2.8mm Calibrant = N/A* |
FlexiMass-SR48 steel targets - P/N: TO-431R00
| | |
| --- | --- |
| *Number of wells:* | *Sample = 48 Calibrant = 3* |
| *Internal diameter of wells:* | *Sample = 2.8mm Calibrant = 2.2mm* |
FlexiMass-DS disposable targets - P/N: TO-430R00
| | |
| --- | --- |
| *Number of wells:* | *Sample = 48 Calibrant = 3* |
| *Internal diameter of wells:* | *Sample = 2.8mm Calibrant = 1.5mm* |
Mass Spectrometry meets Infrared Spectroscopy
**Short Name:** Mass Spec based CIVP IR Spectroscopy
**Instrument Type:** Mass Spectrometry
**Instrument Location:** KCL 3
**Date of Acquisition:** December 2021
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Mass Spectrometry meets Infrared Spectroscopy
### **Structural insights into cold, mass selected ions**
[https://cbic.yale.edu/mass-spectrometry-meets-infrared-spectroscopy](/mass-spectrometry-meets-infrared-spectroscopy)
MS recommendations, method descriptions and software
**Short Name:** MS resources
**Instrument Type:** Mass Spectrometry
**Instrument Location:** KCL 3
**Date of Acquisition:** February 2021
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*Disclaimer: All information on this site is subject to change and the actual experimental methods used might differ from the ones found here!*
**Recommendations:**
[MS\_Sample\_Method\_Recommendations\_v2.docx](/sites/default/files/files/MS_Sample_Method_Recommendations_v2.docx)
**Method Descriptions** (methods might have changed over time, please double-check!):
[Shimadzu 9030 HRMS Description](/sites/default/files/files/Experimental-Method_Shimadzu-QToF-9030_v4.docx)
[Thermo Fisher QExactive Orbitrap HRMS Description](/sites/default/files/files/Experimental-Method_Thermo-QExactive.docx)
**Software:**
**Data exchange**
MS data can be exported as mzXML or mzML files and shared via ***box*** or ***google drive*** upon request. The files contain TIC and MS data, EIC can be extracted through user analysis. These data files can be opened with **MestreNova** (updated and fully installed licenses necessary!):
*Download the software and license bundle from the CBIC homepage:*
[*https://cbic.yale.edu/yale-only/mnova-download*](https://cbic.yale.edu/yale-only/mnova-download)
*Close MestreNova (for update of existing installation), and run as Administrator by:*
*Windows Start menu -> MestreNova Folder -> Right Click on MestreNova -> more -> Run as Administrator*
*Install the Licenses again, close the software and start it as a normal user.*
**Complex data workups** and **simple txt data** can be provided based on the project.
Software for opening and converting ThermoFisher .raw files: <http://msfragger.nesvilab.org/tutorial_convert.html>
**Acknowledgements:**
If you use CBIC instruments in your research, we request that you acknowledge our facility in your written publications or grant applications as follows:
Acknowledgement: *This research made use of the Chemical and Biophysical Instrumentation Center at Yale University (RRID:SCR\_021738). Equipment was purchased with funds from Yale University.\
Optional for Orbitrap QExactive MS: NSF MRI grant CHE-1828190.*\