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United States Department of Agriculture

Agricultural Research Service

Proteomics - Mass Spectrometry
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The mass spectrometry resource at ERRC supports ARS research projects that require identification of peptides, proteins, oligosaccharides, small molecules, lipids, and polymers of biopolymers structural characterization.  Analyses are carried out using high-resolution mass spectrometry (MALDI-TOF/TOF and Q-TOF).  Association of the mass spectrometer instruments with a Nano/Capillary UHPLC results in an LC/MS-MS type of analysis.  Data processing software for peptide/proteins identification include GPS Explorer, ProteinLynx Global Server, Proteome Discoverer, Scaffold, and MASCOT server.



Alberto Nunez Ph.D., Chemist

Voice: (215) 233-6639
FAX:  (215) 233-6796



Request forms:

Request forms and sample processing protocols can be downloaded in PDF format:




Synapt G1 Q-TOF:  Utilizing Electrospay Ionizaion (ESI) or Atmospheric Pressure Chemical Ionization (APCI) analysis can be performed from small molecules (150 to 1000 Da) to peptides and proteins.  The Q-TOF instrument offers a power resolution (FWHM) of 8000 and 18000, and a mass accuracy with an error >5 ppm.  Operational modes include Ion Mobility Mass Spectrometry, MS/MS and MSe.  The analyses are done by infusion or by 1D or 2D UHPLC.



Q-TOF Synapt G1 Mass Spectrometer


4700 Proteomics Analyzer - MALDI-TOF/TOF:  This instrument offers a high power resolution (FWHM = 20,000) with a mass accuracy of >50 ppm across the plate with external calibration and >2 ppm with internal calibration.  The ability to obtain Peptide Mass Fingerprints (PMF) combined with tandem mass spectrometry (MS/MS) of selected peptides provide a powerful tool for proteins and peptides identification through database searching or de novo sequencing.


MALDI-TOF/TOF is particularly useful for identification of protein spots in electrophoresis gels.  The instrument is associated with the MASCOT automated database search software for proteins identification with GPS Explorer Software.  MALDI-TOF/TOF analysis is also extended to oligosaccharides and polymers.



4700 Proteomics Analyzer Mass Spectrometer with GPS Explorer Software


1D and 2D UHPLC:  This instrumentation allows the use of nano-columns (75 µm and 100 µm), capillary columns (300 µm) and 1 mm columns.  The 1D instrument operates in association with the Q-TOF mass spectrometer, and UV detector, or with a LC Packings Probot for MALDI plate spotting or sample fractioning.  The 2D system is dedicated to bottom-up proteins identification (shotgun proteomics) with the Q-TOF mass spectrometer.



1D-Nano/Capillary-Acquity UHPLC with UV Detector



2D-Nano-Acquity UHPLC



LC Packings Probot Fraction Collector

Last Modified: 9/7/2017
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