Mass Spectrometry Analysis

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Analytical Services
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  •  LC-ESI-MS/MS, Thermo LTQ Orbitrap XL with ETD System
  • Q-STAR Applied biosystems, Inc.
  • Q-TOF Waters



  • Highly functional equipment for LC-MS process
  • Mixed protein analysis using Turbo SEQUEST software
  • MS coupled with nano LC
  • Sensitivity : fmol range


1. Confirm the MALDI-TOF data
2. Immunoprecipitation and pull-down sample identification
3. Mixed protein
4. Recombinant protein identification (in the SDS-PAGE gel)



  • MALDI-MS, Applied Biosystems Voyager-DE STR
  • MALDI-MS, Bruker Daltonics microflex LRF20



  • Automation of all processes and data processing
  • High accuracy and Post-Source Decay (PSD) establishment
  • Flexible data acquisition and processes using DataExplore software
  • Sensivibity : fmole
  • Accuracy : < 10 ppm


1. Identification of 2 DE gel spot and high purity protein
2. Confirm the molecular weight of protein. Intact mass service
3. Modified protein identification

Peptide Mass Finger Printing

The proteins are cut into several fragments using proteolytic enzymes such as trypsin, chymotrypsin, etc. The proteolysis is typically carried out overnight and
the resulting peptides are extracted with acetonitrile and dried under vacuum.
The peptides are then dissolved in a small amount of trifluoroacetic acid based buffer or further concentrated and purified using ZipTipTM tips and are ready for mass spectrometric analysis.

The digested protein can be analyzed with different types of mass spectrometers such as ESI-TOF or MALDI-TOF. MALDI-TOF is often the preferred instrument because it allows a high sample throughput and several proteins can be analyzed in a single experiment.


Protein Identification

ProteomeTech offers protein identification by most modern mass spectrometric techniques. To ensure highest sensitivity and reliability, ProteomeTech uses mostly nano LC-ESI-MS/MS and MALDI-TOF MS (Applied Biosystems Voyager-DE STR) which allows unequivocal identification of one and more proteins within
a sample. This is very suitable for analysis of protein bands from SDS-PAGE, protein complexes and other low or medium complex protein samples.

Protein identification results will be provided electronically in one report including protein name, amino acid sequence and molecular weight.
The target protein can be identified by comparing the peptide mass fingerprinting to protein databases.


Intact Mass Measurement

The protein identification service is applied to protein samples delivered as protein gel spot, protein gel band, lyophilized, in solution or bound to blotting membrane. Proteins are either analyzed by MALDI-TOFTOF-MS or nano LC-ESI-MSMS.

For maximum protein identification success rate, we recommend 2-D electrophoresis in 1 pH range and using Coomassie blue G250 or Sypro-Ruby staining (success rate: more than 90%). If silver staining of the gel is not convenient, MALDI compatible silver staining (mentioned below) must be used. Also, spots obtained in this way must be consulted with ProteomeTech staff before requesting for identification.


De novo peptide sequencing

We offer a de novo peptide sequencing service using LC coupled ESI-MS/MS (Thermo LTQ Orbitrap XL with ETD System).

Purified proteins or gel spots from 2 DE gel are trypsinized into peptides with in-gel or in-solution digestion. The tryptic peptides are analyzed and compared with existing amino acids sequences in the data bases. Usually, we offer analysis of amino acids sequence more than 3 peptides and 8 to 14 amino acids in a peptide. If there is few information of peptide fingerprinting, we analyze the protein spot with this method.

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