Mass Spectrometry Service

Our Mass Spectrometry facility has over 15 years of experience handling all sample types (cells, tissues, protein extract, serum, IP, etc). Our services cover from customized mass spectrometry sample prep to liquid chromatography and mass spectrometry protocols designed for each application. By employing top-of-the-line Orbitrap Exploris technology, we offer low cost, high sensitivity and high accuracy Mass Spectrometry analysis.

Please use the table below to guide you in choosing the right service

Mass Spec ServiceSample TypesStudy ObjectivesData Report
IDQuantPTM
Protein Identification 1
nanoLC-MS/MSAll typesIdentify all proteinsxOpt.Opt.
MALDI-TOF/TOF1D/2D bandsIdentify top protein hitxOpt.
Protein Identification & Quantitation 2
Label Free Quan (LFQ)All typesID & quantify all proteinsxxOpt.
Data Independent Acquisition (DIA)All typesID & quantify all proteinsxx
Single Cell ProteomicsCellsID & quantify proteins in a single cellxxOpt.
iTRAQ QuantitationAll typesID & quantify proteins by iTRAQ labelxxOpt.
TMT QuantitationAll typesID & quantify proteins by TMT labelxxOpt.
Post Translational Modification Sites (PTMs) 3
Phospho-SitesPurified / IPIdentify Phospho sitesxx
Other PTM sitesPurified / IPIdentify PTM sitesxx

1. Protein Identification

We offer two workflows for protein identification: nanoLC-MS/MS and MALDI-TOF/TOF

  • In nanoLC-MS/MS, digested peptides from protein mixtures are first separated in a nano-flow LC, then subject to high-resolution orbitrap mass spectrometry. This approach is ideal for identifying all proteins in a protein mixture ranging from 1D gel bands to cell lysates.
  • In MALDI-TOF/TOF, digested peptides from a single protein are directly subjected to peptide finger print (MS) followed by fragmentation (MSMS) of top precursors. This approach is ideal for identifying a single protein in 2D gel spots selected from upstream 2D DIGE analysis.

2. Protein Identification and Quantitation

We offer both label-free quantitation (LFQ) and labeled quantitation (iTRAQ, TMT). We have optimized both workflows along with our high-resolution mass spectrometry to ensure the highly sensitive detection and accurate quantitation of all proteins in each sample.

We offer both data-dependent (DDA) and data-independent (DIA) analysis. DDA is performed on Proteome Discoverer 2.5 whereas DIA is performed on DIA-NN.

3. Post-translational Modification (PTM) site identifications

We offer PTM site identification services for the popular PTMs such as phosphorylation, acetylation, and methylation. Other types of PTMs are also covered.

FAQ

Frequently asked questions about Mass Spec features, process, time & cost:

Our Protein ID by MALDI-TOF/TOF has almost 100% success rate following our 2D DIGE analysis.

Our Protein ID by LC-MS/MS can detect almost all proteins in any protein samples.

There are many factors that may affect a successful identification. The main factors are: low protein amount; samples containing multiple proteins (for MALDI-TOFTOF); proteins with significant amount of PTMs or chemical modifications, very hydrophobic proteins and proteins with few tryptic sites. Samples with only one protein are well-suited for MALDI-TOF/TOF, while samples with multiple proteins are ideal for LC-MS/MS.

In nanoLC-MS/MS, digested peptides from protein mixtures are first separated in a nano-flow LC, then subject to high-resolution orbitrap mass spectrometry. This approach is ideal for identifying all proteins in a protein mixture ranging from 1D gel bands to cell lysates.

In MALDI-TOF/TOF, digested peptides from a single protein are directly subjected to peptide finger print (MS) followed by fragmentation (MSMS) of top precursors. This approach is ideal for identifying a single protein in 2D gel spots selected from upstream 2D DIGE analysis.

Label-free quantitation uses the number of spectra or the intensity of spectra to compare the relative abundance between samples. Due to the high sensitivity of Orbitrap Mass Spectrometry and sophisticated Proteome Discoverer software, this is a reliable approach that is more straightforward than labeled methods.

TMT and iTRAQ use isobaric tags to label all peptides in a sample. Although the tags have the same total mass, the reporter regions have different masses. These differences are detected by the mass spectrometer after the fragmentation step in MS/MS, allowing highly accurate and precise quantitation.

The DDA approach fragments only peptide precursors meeting certain criteria, and searches against a protein database.

The DIA approach fragments all peptides across a precursor window, and searches the precursors against a spectral library database.

Although DIA produces more hits, it can generate more false positives than DDA. In addition, the time it takes software to process DIA data is significantly longer than for DDA.

2D DIGE followed by MALDI-TOF/TOF has a sensitivity of 1 fmol.

Our LC-MS platform has a max resolution of 240,000 FWHM and dynamic range of 5 orders, allowing even the lowest abundance proteins to be detected.

5-7 days.