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Small Molecule Mass Spectrometry Facility (FAS)

Director: Trauger, Sunia

Location: Northwest Laboratory building, B2, 52 Oxford Street, Cambridge, MA, 02138


The Small Molecule Mass Spectrometry Facility at the FAS Center for Systems Biology offers support for the analysis of a wide variety of analytes using mass spectrometry based techniques. We are located in the second basement (B2) level of the Northwest Laboratory building at 52 Oxford Street, Cambridge, MA 02138. We provide services for molecular formula confirmation (accurate mass measurement), structural elucidation (MS/MS) and quantitation of small molecules. In addition, we can assist you in the mass analysis of a wide variety of non-proteomics samples including metabolites, medium sized proteins and oligonucleotides. Please contact us and tell us about your samples prior to submission or use of our Open Access laboratory.





  • Agilent 1100 HPLC with UV Detector ( Chromatography instrument )

    This stand alone HPLC comes with a diode array detector and can be used on an open access basis by Harvard personnel.

  • Agilent 6120 Quadrupole LC/MS with Multimode Source ( Liquid chromatography mass spectrometry platform )

    This instrument is not open access. Samples can be run on a fee-for-service basis. "This quadrupole mass spectrometer is equipped with a multi-mode source that can be used both in APCI and ESI modes for the ionization of a diverse range of compounds. This instrument is useful for quantitation in selected ion monitoring mode (SIM) and has a large dynamic range. It comes with its own HPLC system and fraction collector"

  • Agilent 6210 Time-of-Flight LC/MS ( Liquid chromatography mass spectrometry platform )

    Open access instrument for investigators, after brief training. This instrument provides high resolution data (20,000 resolving power at m/z=622) and high accuracy ~ 5 ppm RMS error suitable for formula confirmation of small molecules. It is also used for protein analysis using LC-MS due to its large mass range. Deconvolution software (MaxEnt) allows the interpretation of high charge states produced for protein samples.

  • Agilent 6460 Triple Quadrupole Mass Spectrometer with Agilent 1290 uHPLC ( Liquid chromatography mass spectrometry platform )

    This LC-MS/MS instrument is expected to boost our capacity for sensitive and accurate quantitation of molecules using multiple reaction monitoring (MRM) and other mass spectrometry techniques that allow the highest dynamic range (5 to 6 orders of magnitude) and most sensitive measurements possible at an expanded MW range of 50-3200 m/z. Other unique experiments which can be performed on this high performing triple quad mass spectrometer include precursor ion scanning, neutral loss scans etc. which can target a specific class of compounds in a sample depending on its tandem MS pattern. It comes with an Agilent 1290 uHPLC which can be used for rapid and sensitive HPLC methods development using ultra high performance (and pressure) HPLC. The new Jetstream electrospray source and an atmospheric pressure chemical ionization (APCI) source will allow maximum flexibility in monitoring a range of molecules. This instrument is expected to be a crucial tool for targeted metabolomics research. This instrument will be operated on a fee-for-service and collaborative basis.

  • Bruker Maxis Impact q-TOF Mass Spectrometer ( Liquid chromatography mass spectrometry platform )

    This is a quadrupole time of flight mass spectrometer with both a ESI and APCI interface. This high resolution tandem mass spectrometer which can be used to get high small molecule ID and metabolomics experiments. High resolution can be achieved in both MS and MS/MS modes for identification and formula confirmation. Samples are submitted for fee-for-service analysis. No open access!

  • TSQ Quantum Access MAX Triple Stage Quadrupole Mass Spectrometer ( Liquid chromatography mass spectrometry platform )

    Fee for service instrument. The Thermo triple quad mass spectrometer has a m/z range of up to 1500 and is optimal for small molecule quantification. It is coupled to a HPLC and autosampler. Custom methods can be developed for users for a minimal hourly rate and samples analyzed. Please see our website for rates.

  • Waters MALDI-TOF ( Mass spectrometer )

    This easy to use matrix assisted laser desorption ionization (MALDI)-time-of-flight mass spectrometer is open for users by investigators after brief training. Samples ranging from small molecules to proteins can be analyzed using this instrument in a rapid and affordable analysis.

  • Waters Quattro micro GC/MS/MS ( Mass spectrometer )

    Open access instrument to Harvard University investigators, after brief training. This is a GC-MS/MS mass spectrometer that incorporates a triple quad mass analyzer and GC separation for volatile organics.


  • High Resolution LC-MS ( Material analysis service )

    Samples will be analyzed using high resolution mass spectrometry. Interpreted data report will be provided to the user ~24 hours after sample submission. This service is available to all.

  • Mass Spectrometry Analysis ( Material analysis service )

    Fee-for-service MS Analysis

  • Protein LC-MS Analysis ( Material analysis service )

    LC-MS will be used to analyzed proteins of interest. Interpreted report providing accurate MW information (typically within 1 Da) will be provided to the investigator. This technique is ideal for studying covalent attachments to proteins of interest.

  • Quantitative Analysis of Small Molecules ( Material analysis service )

    Using standard compounds, an optimum HPLC-MS/MS method will be developed for the molecule/molecules of interest. After this samples will be quantified using a standard curve based on internal or external standards on a triple quadrupole mass spectrometer.


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Last updated: 2012-07-12T12:58:40.299-04:00

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The eagle-i Consortium is supported by NIH Grant #5U24RR029825-02 / Copyright 2016