Protein Identification

Our protein identification services by Mass Spectrometry offer almost 100% success rate, by employing the latest technologies and optimized protocols. Customers can choose from the following:

  • NanoLC-MS/MS: Identify ALL proteins in a mixture ranging from 1D gel bands, subcellular organelles, IP, secretome to whole cell lysate or tissues. We also offer Label Free Quantitation for protein quantitation.
  • 2D Gel Spots: Identify a single protein in 2D spots (or 1D gel bands). This is often used to identify protein spots showing differential expression after 2D DIGE.

Sample category for nanoLC-MS/MS:

  1. Low complexity samples: 1D gel band – contain only one gel piece with one protein band, <10 proteins
  2. Moderate complexity samples: protein mixture such as column purified sample, <100 proteins
  3. Moderate to High complexity samples: Protein mixtures such as IP samples, secretome, subcellular organelles such as mitochondria, endoplasmic reticulum, lysosomes etc
  4. High complexity samples: whole cell lysate, tissue, and others

nanoLC-MS/MS Procedure

LCMSMS procedure: step 1 - in gel or in solution samples

Protein Mixture (1D Gel bands or Liquid samples)

LCMSMS procedure: step 2 - Protein Fractionation by pI or Mw

Protein Fractionation by pI or Mw (optional)

LCMSMS procedure: step 3 - Reduction/alkylation & Trypsin Digestion

Reduction/alkylation & Trypsin Digestion

Abundance spectra detected by MS over the LC gradient


LCMSMS procedure: step 6 - Database Search for Protein ID

Database Search for Protein ID

NanoLC-MS/MS Procedure:

  1. Optional sample prep: Protein fractionation by either pI or molecular weight for high complexity samples. We also offer serum abundant protein depletion. We recommend Serum 2D DIGE for all serum and plasma samples.
  2. Sample prep: Sample clean up & concentrating (if needed), followed by measuring protein concentration
  3. Trypsin digestion: Reduction, alkylation and trypsin digestion
  4. NanoLC-MSMS: Digested peptides are separated on a nano-flow Ultimate 3000 and analyzed by Orbitrap Exploris high-resolution mass spectrometer
  5. Data analysis by Proteome Discoverer. For DIA experiments, analysis is performed using DIA-NN.

In-solution Samples

Sample type: We accept in-solution, in-gel samples or IP beads for this service.

Protein amount: 5-200 µg of total protein from each sample. For 1D gel bands, 5-20 ng protein / band is preferred.

Protein concentration: 5-20 mg/ml is preferred for in-solution samples.

Buffer: Please feel free to submit samples in whichever buffer that you would normally use.  Please inform our scientists about buffer composition. Additional charge may apply on samples that require extensive amount of the extra work such as protein eluting, concentrating, buffer exchange or serum abundant protein depletion.

Biohazardous Materials: We do NOT accept samples containing any biohazardous materials. If your samples contain any biohazardous materials, please make sure to deactivate them completely using the appropriate procedure and declare them in the order form. In addition, we do NOT accept any samples containing Level 4 biohazardous materials even if they are deactivated. Please view here for the rank of biohazardous materials.

Sample type: Please inform our scientists about your sample type. We will send you additional tips for each sample type.


Services DescriptionAcademic/Governmental LabsIndustrial/Commercial Labs
Protein Fractionation355Acall for price355Ncall for price
LC-MS/MS on Low Complexity Samples
(1D Gel band, 3-5 samples)
LC-MS/MS on Low Complexity Samples
(1D Gel band, 6 or more samples)
LC-MS/MS on Moderate Complexity Samples332Acall for price332Ncall for price
LC-MS/MS on Moderate to High Complexity Samples334Acall for price334Ncall for price
LC-MS/MS on High Complexity Samples333Acall for price333Ncall for price

Each order should have a minimum of 2 samples (minimum of 3 if low complexity). Turnaround time is ~7 business days.

Sample category:

  • Low complexity samples: 1D gel band – Each sample should contain only one gel piece with one protein band, no bigger than 1x1x5mm in size, <10 proteins. Samples with more than one gel piece, and/or more than one protein band will be considered as moderate to high complex samples. We recommend you cut out only the area with your protein of interest (1x1x2mm size) and follow these guidelines to prepare samples
  • Moderate complexity samples: protein mixture such as column purified sample, <100 proteins 
  • Moderate to High complexity samples: Protein mixtures such as subcellular organelles, IP samples
  • High complexity samples: whole cell lysate, tissue, and others

Price covers the following:

  • NanoLC-MSMS
  • Standard database search against one species in NCBI or SwissProt database using SequestHT

Price does NOT cover:

  • Sample preparation
  • Data request in addition to the standard report