Mass spectrometry can be used for analysis of small molecules, oligonucleotides, lipids, glycans, proteins, peptides and determining the location of post translational modifications. It offers accuracy of measurement over a wide molecular weight range, as small as sub-picomole, sample consumption. Furthermore, any difference between theoretical and measured mass may provide important information about the primary structure and post-translational modifications of a therapeutic protein product.

Mass spectrometery is used for the analysis of macromolecules originating from biological sources, such as proteins, peptides, DNA or RNA oligomers. Instrumentation of mass analysis has experienced tremendous improvements in recent years. Electrospray-ionization mass spectrometry (ESI-MS) and matrix assisted laser desorption time-of-flight mass spectrometry (MALDI-TOF MS) have become the methods of choice for the analysis of pharmaceuticals and biosimilars. Both techniques are powerful analytical tools by themselves, but are most powerful if used in combination with techniques such as gel electrophoresis, electro-blotting, liquid chromatography (LC), capillary electrophoresis (CE) and/or protein sequencing. These two techniques are now the major technologies used in metabolomics and proteomics.

Bio-Synthesis offers a wide range of analysis

  • LC-MS/MS
  • Peptide mass fingerprint analysis
  • Post-translational modification identification
  • Stable isotope related procedures ( iTRAQ, and 18O and SILAC)
  • Oligonuclotide LC-MS Analytical Services
  • Oligonuclotide LC-MS Analysis of Long & Large Oligonucleotides
  • Oligonucleotide LC-MS of single stranded oligonucleotides (ssDNA and ssRNA), double stranded oligonuclotides (ds DNA and dsRNA as well as hybrid duplexes)
  • Peptide LC-MS
  • Peptide LC-MS/MS
  • LC-MS/MS for Protein & Peptide Identification

Bio-Synthesis' mass spectrometry services uses industry-leading technologies—instruments, chemistry, software, and quantification tools -- that are specifically optimized for exceptional, application-focused performance. This end-to-end system is designed to deliver the fast and reliable quality control methods for your proteins and peptides.

Please contact us to discuss your specific project in more detail. We will provide you with a full project proposal within 2 days that includes analysis protocols, timelines, and costs.

Identify and QA your protein/peptide by MS starting at $250

Services and Fees

Price subject to change based on project specifications. Contact us for services and fees not listed below.

Services Cost/Sample
Electrospray Mass Spectrometry Analysis
Electrospray Mass Spectra (ESI) Starting at $300
ESI-MS/MS Starting at $350
Liquid Chromatography Mass Spectra (LC-MS) Starting at $350
Liquid Chromatography Mass Spectra (LC-MS/MS) Starting at $600
MALDI Mass Spectrometry Analysis
MALDI-TOF-MS Starting at $350
Protein / Peptide Analysis Services
SDS-PAGE, 1D Starting at $250
IEF Starting at $250
RP HPLC (proteins or peptides from 1,000 to 70,000 dalton) Starting at $250
Desalting $150
Trypsin Digest $150
HPLC DAD (Photo Diode Array UV-vis) Starting at $350
Peptide Mapping using HPLC Starting at $600

Mass Spectrometry Core Equipment

  • Applied Biosystems Voyager-DE STR MALDI-TOF
  • Applied Biosystems Voyager MALDI-TOF
  • Thermo LTQ XL LC-MS Mass Spectrometer
  • Thermo LTQ XL LC-MS/MS Mass Spectrometer
  • Thermo LTQ XL LC-MS/MS Mass Spectrometer with capillary LC system

Quality Control

Data quality is ensured through the use of appropriate internal and external standards. The MALDI-TOF mass spectrometers are calibrated with external standards that vary depending on the analyte molecular weight. This results in the best calibration for the most accurate mass assignments. Samples that have been trypsin digested are internally recalibrated from observed trypsin autolysis fragments. The electrospray mass spectrometers are calibrated using polyalanine which allows for even distribution of multiple mass peaks. A variety of search engines, for protein identification from mass fingerprinting and for interpretation of MS/MS spectra, are available each of which generates its own statistics. The choice of database searching software to be applied is optional to investigators and discussion of this matter is encouraged with our technical support team.

Sample Submission and Ordering

Sample Storage

  • Lyophilize or speed vac to a solid sample to ensure stability during shipment. Store sample in Eppendorf Safe Lock tube packed in such a way that the sample is cushioned from the effects of FedEX. If a gasket-equipped tube is not available, use Parafilm to assure that the cap does not pop off in shipping. Keeping the sample cool is at the discretion of the investigator. It may not be necessary to preserve biological activity or structural integrity of the sample unless solubility will become an issue. Dried samples and samples on PVDF do not require being kept cool.
  • Alternatively, refrigerate to +4°C for cold shipment of the liquid sample.

Sample Shipment

  • Please provide amounts of 1 to 3 µgs and higher per oligonucletide, peptide or protein in lyophylized as a dry powder form. If possible ship sample frozen in aqueous solution containing volatile buffers. If this is not possible an additional sample handling step may be needed.
  • Before sending a sample, please use the mass spectrometry sample submission form to alert us for the arrival of the sample. Concurrently, a printed copy of the mass spectrometry sample submission form should accompany the sample. This form is available on this website and can be filled out online.
  • Ship the sample to:
Bio-Synthesis Inc
Bioanalytical Laboratory
Attn: Mass Spectrometry
800 Mario Court
Lewisville, TX 75057
800.227.0627 | 972-420-8505

Mass Spectrometry Sample Preparation Guidelines

Prior to sending samples, investigators are recommended to contact the facility to discuss the required analysis. This is necessary to ensure that the most efficient and cost-effective analytical methods are employed. Samples are normally analyzed in the order of their receipt, but special arrangements can be made for unstable samples.

A sample submission form should accompany each set of samples

General guidelines for sample preparation:

When preparing samples for mass spectrometric analysis, it is best to limit sample manipulations. When dealing with solution samples, never bring the sample to complete dryness. Salts and detergents will interfere with MS analysis of solution samples. Based on extensive studies, we have found that SDS-PAGE or 2D IEF-SDS-PAGE is the best method for recovery of low quantities of protein.

  1. The sample should be dissolved in pure water or shipped completely dry if possible. Try to avoid sending samples in high ionic strength buffers as this may interfere buffers, such as PBS, are well known for suppressing the ionization process and should be avoided if possible.
  2. If the sample is shipped in solution containing any salt, please provide an estimate of the salt concentration possible. Also, providing a list of the salts and buffers that might be present in the solution is also extremely helpful.
  3. Any amount of sample can be submitted for analysis. Due to the fact the ionization process and detector sensitivity are sample dependent, it is rather difficult to specify a minimum amount of sample necessary for analysis. The general rule of thumb is, "The more the better".

    Sample amount recommendation:

    Sample Requirements and Shipping:

    Please provide amounts of 1 to 3 µgs and higher per oligonucletide, peptide or protein in lyophylized as a dry powder form. If possible ship sample frozen in aqueous solution containing volatile buffers. If this is not possible an additional sample handling step may be needed.

    LC MS/MS
    • Please provide estimated or exact molecular mass for your sample if known.
    • Alternatively, provide the molecular range in which the molecular mass is expected.
    • Provide sample amounts of 1 to 3 µgs or more.
    • For protein identification via LC-MS/MS coomassie blue stained and digestion compatible silver stained protein bands are appropriate.
    • LC-MS/MS allows analysis of complex peptide and protein mixtures. Call for info for more details.

    • Suitable for intact protein mass analysis.
    • Analysis of DIGE protein spot digestion is possible.
    • A variety of biomolecules can be analyzed including oligosaccharides, and gangliosides.
  4. Please provide information regarding the sample. This includes information such as sample type (peptide, protein, etc.), expected molecular weight, purity, etc.
  5. Radiolabeled samples may not be submitted for mass analysis.


Protein/peptide solutions in 10 μM volatile buffers can sometimes be analyzed directly while samples with higher salt concentrations require prior C18 or C4 ZipTip desalting.

Links and Resources

Order Form
Mass Spectrometry Online Order Submission Form
Useful Links

Selected Reading
  1. Mann, M., Kelleher, N.L., Precision Proteomics: The case for high resolution and high mass accuracy, Proc Natl Acad Sci U S A. 2008 Nov 25;105(47):18132-8.
  2. Graumann, J., et. al., SILAC-labeling and proteome quantitation of mouse embryonic stem cells to a depth of 5111 proteins, Mol Cell Proteomics. 2008 Apr;7(4):672-83. Epub 2007 Nov 28.
  3. Walker, J.M., The Proteomics Protocols Handbook, 2005 Simpson, R.J., Purifying Proteins for Proteomics: A Laboratory Manual, 2004.
  4. Haas, W., et. al., Optimization and use of peptide mass measurement accuracy in shotgun proteomics, Mol Cell Proteomics. 2006 Jul;5(7):1326-37. Epub 2006 Apr 23.
  5. Walker, J.M., The Proteomics Protocols Handbook, 2005 Simpson, R.J., Purifying Proteins for Proteomics: A Laboratory Manual, 2004.