Services and Fee Schedule

Upstate Investigators

Before preparing the samples, please read the sample preparation guidelines and requirements for an application of interest or contact the facility.

Consultations are free.

Service Type Unit Price, $
Trypsin digestion* 15
Microscale cleanup 10
MW determination
Protein identification ** short gradient 60
medium gradient 108
long gradient 180
Protein profiling iTRAQ,
TMT, or SILAC analysis
1D 200
2D 2400
Method development 60/h
Data analysis 60/h
Small molecule quantification short run 17
long run 30

*-Full price = (Number of units) x (Unit Price) + ($35 Setup Price)
**- Add additional $10.00 per PTM to the full price

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Trypsin Digestion

Proteolytic digestion is prerequisite for protein identification and quantification by LC/MS/MS analysis. Proteins are digested in solution or in gel band/spot.

Trypsinization of protein samples is required for protein identification and protein profiling. Trypsinization can be performed by the facility user or by facility staff for an extra charge of $15 per sample and a one time set up fee of $35. The charge for a typical protein ID from SDS-PAGE gel is $108 (medium length run) and, if trypsinization is performed by facility staff, an additional $50 for the first sample (plus $15 for each additional sample).

The following services are provided for trypsin digestion:

Service Service Code Fees Sample Requirements
In-gel tryptic digestion (for following LC/MS/MS analysis) 100  $35/set-up
+ $15/sample
  • Gel thickness: 1mm (1mm spacer)
  • Total protein in a sample: a protein band or spot visible by coomassie or Sypro Ruby staining
In solution tryptic digestion (for following LC/MS/MS analysis)
  • Total protein in a sample: ≥ 0.1 picomole/protein
  • Total protein concentration in a sample: ≥ 0.05 mg/ml
  • Sample buffer: 50 mM ammonium bicarbonate NH4HCO3 or Tris-HCl, pH 8.1-8.5
  • Samples should not contain detergents

Molecular Mass Determination

Dissolved analyte (protein, peptide, small molecule) is infused into a mass spectrometer, the mass to charge ratios (m/z) are measured, and the molecular masses are determined. Volatile solvents facilitating positive (proteins, peptides, small molecules) or negative (small molecules) ionization of analytes are used.

The following services are provided:

Service Service Code Fees Sample Requirements
MS analysis - direct sample infusion; determination of the molecular mass of an analyte (small molecule, protein, or peptide).
200
$50/sample
  • Samples can be submitted either as soluble lyophilized powder or in solution with adequate volatile buffer
  • Analyte concentration > 5 µM
  • Protein/peptide sample buffer: 0.1% formic acid, 5% (or higher) acetonitrile
  • Samples should not contain detergents, non-volatile salts, etc.

Protein Identification

Proteins are identified through identification of the peptides unique to a protein. Peptides, in turn, are identified through fragmentation and determination of the corresponding fragment masses. A protein or protein mixture is digested by trypsin to generate tryptic peptides. Tryptic peptides are analyzed by mass spectrometry in line with reverse phase HPLC. Peptides are separated on an HPLC column and eluted peptides are analyzed in a mass spectrometer: peptide masses (m/z, mass per charge) are determined (MS spectrum), then, each analyzed peptide is fragmented and the corresponding fragment masses are determined (MS/MS spectrum). The MS/MS spectrum of each analyzed peptide is submitted to database search for identification. A peptide (sequence) is identified by comparison of its MS/MS spectrum to the MS/MS spectra generated by software for all tryptic peptides of all database proteins A unique set of identified peptides (derived from the same parent protein) identifies the corresponding parent protein.

The following services are provided for protein identification:

Service Service Code Fees Sample Requirements
LC/MS/MS analysis of digested protein samples
  • Total protein in a sample: ≥ 0.1 picomole/protein
  • Total protein concentration in a sample: ≥ 0.05 mg/ml
  • Sample should not contain detergents
  • Short Run (0.5 hr. gradient)
300
$60/run
  • Medium run (1 hr. gradient)
301
$108/run
  • Long run (2 hr. gradient)
302
$180/ run

Mapping of Specified PTMs

Proteins are identified through identification of the peptides unique to a protein. Peptides (with or without PTM), in turn, are identified through fragmentation and determination of the corresponding fragment masses. A protein or protein mixture is digested by trypsin to generate tryptic peptides. Tryptic peptides are analyzed by mass spectrometry in line with reverse phase HPLC. Peptides are separated on an HPLC column and eluted peptides are analyzed in a mass spectrometer: peptide masses (m/z, mass per charge) are determined (MS spectrum), then, each analyzed peptide is fragmented and the corresponding fragment masses are determined (MS/MS spectrum). The MS/MS spectrum of each analyzed peptide is submitted to database search for identification. The peptide sequence and the residue bearing (if any) a specified PTM is identified by comparison of the peptide MS/MS spectrum to the MS/MS spectra generated by software for all tryptic peptides of all database proteins. A unique set of identified peptides (derived from the same parent protein) identifies the corresponding parent protein.

The following services are provided for mapping of specified PTMs:

Service Service Code Fees Sample Requirements
LC/MS/MS analysis of digested protein samples
  • Total protein in a sample: ≥ 0.1 picomole/protein
  • Total protein concentration in a sample: ≥ 0.05 mg/ml
  • Sample should not contain detergents
  • Short Run (0.5 hr. gradient)
400
   $60/run
+ $10/PTM
  • Medium run (1 hr. gradient)
401
  $108/run
+ $10/PTM
  • Long run (2 hr. gradient)
402
   $180/run
+ $10/PTM

Protein Profiling - iTRAQ Analysis

Protein profiling determines the molar ratios (relative abundance) of identical proteins in compared complex protein mixtures (protein samples). Using iTRAQ analysis, the relative abundance of proteins can be determined in up to eight protein extracts at a time (per analysis). This is achieved by labeling of multi-protein extracts using 8 mass spectrally resolvable, charge-matched labels. iTRAQ labeling is conducted using a commercial kit (Applied Biosystems, Foster City, CA) according to the manufacturer’s protocol. Equal amounts (20-100 µg) of total protein from each sample are separately digested with trypsin and labeled with one of iTRAQ reagents (iTRAQ tags are covalently linked to the amino group of the lysine and/or the N-terminal residues of tryptic peptides). The labeled samples are pooled and analyzed by LC/MS/MS for protein identification and quantitation:  identical peptides with different iTRAQ tags are resolved in the same chromatographic peak, the masses of eluted peptides are determined, then, the peptides are fragmented and the fragment masses, as well as, the intensities of the released iTRAQ tags are determined. If losses occur during analysis, each sample experiences the same loss and the ratios (relative abundance) of identical peptides are preserved. The acquired MS data is submitted to database search; the sequence of each analyzed peptide is identified and the relative abundances of identical peptides with different tags are determined. Identified peptides determine the identity and the relative abundance of the corresponding parent proteins.

The following services are provided for iTRAQ analysis:

Service Service Code Fees Sample Requirements
LC/MS/MS differential protein expression analysis of iTRAQ labeled/digested samples
500
$200/run
  • iTRAQ labeling should only be performed using a commercial kit according to the manufacturer's protocol; collected labeled samples are ready for the following LC/MS/MS analysis and can be stored at -20ºC
iTRAQ labeling (for following LC/MS/MS differential protein expression analysis)
  • Total protein in a sample: 20-100 ug
  • Total protein concentration in a sample: 1-5 mg/ml
  • Sample buffer: 0.5 M TEAB (triethylammonium bicarbonate), pH 8.5, 0.1% SDS
  • Samples should not contain primary amines, thiols (mercaptoethanol, DDT, etc)
  • 2-plex (set of 2 samples)
502
$350
  • 4-plex (set of 4 samples)
504
 $650
  • 8-plex (set of 8 samples)
508
 $1200

Protein Profiling - SILAC Analysis

Protein profiling determines the molar ratios (relative abundance) of identical proteins in compared complex protein mixtures (protein samples). SILAC - stable isotope labeling by amino acids in cell culture is used for in vivo labeling of proteins for MS-based quantitative proteomics;  proteins are labeled through metabolic incorporation of ‘light’ or ‘heavy’ form of a given amino acid (usually L-Lysine, L-Arginine). ‘light’ and  ‘heavy’ forms of an amino acid  are chemically identical but differ in content of stable isotopes (usually 13C, 15N), i.e. SILAC labels are mass spectrally resolvable. Two cell populations are grown in media with different labels and labeled protein samples are isolated. Equal amounts of protein samples are pooled and digested by trypsin. Pooled labeled tryptic peptides are analyzed by LC/MS/MS for sequence identification and quantitation:  identical ‘light’ and ‘heavy’ peptides derived from different samples are resolved in the same chromatographic peak, the masses and the intensities of eluted peptides are determined for quantification, then, the peptides are fragmented and the corresponding fragment masses are determined for sequence identification. The acquired MS data is submitted to database search: the sequence of each analyzed peptide is identified and the relative abundances of identical ‘light’ and ‘heavy’ peptides are determined. If losses occur during analysis, each sample experiences the same loss and the ratios (relative abundance) of identical ‘light’ and ‘heavy’ peptides are preserved. Identified peptides determine the identity and the relative abundance of the corresponding parent proteins.

The following services are provided for SILAC analysis:

Service Service Code Fees Sample Requirements
LC/MS/MS differential protein expression analysis of SILAC labeled/digested samples 500 $200/run
  • SILAC labeling should only be performed using a commercial kit according to the manufacturer's protocol. Equal total amounts of labeled proteins (> 5 µg) are mixed and digested with trypsin; digested samples (free of detergents) are ready for LC/MS/MS analysis and can be stored at -20ºC.

Small Molecule Quantification

Samples (cell lysate, body fluids) depleted of macro molecules are submitted to the facility. Small molecules of interest are quantified in submitted samples using LC/MS/MS approach. Analytes are separated by HPLC and monitored by tandem mass spectrometry using volatile solvents facilitating negative or positive ionization of the analytes. The mass to charge ratios (m/z) of intact analytes and corresponding MS/MS fragments are determined; the abundance (signal intensity) of an MS/MS fragment unique to a given analyte is used for its quantification. Calibration standards are analyzed in parallel. A calibration curve is used for quantification of corresponding analyte in the samples. Usually, an internal reference is added to all samples and calibration standards to an identical final concentration.

The following services are provided for small molecule quantification:

Service Service Code Fees Sample Requirements
Samples and calibration standards are submitted to the facility for quantitative analysis of specified small analytes by LC/MS/MS. Clear extracts/solutions free of macro molecules in solvents facilitating negative or positive ionization of the analytes
  • Standard run (up to 15 min)
700 $17/run
  • Long run (up to 30 min)
701 $30/run

Other Applications

Please contact the facility for applications not listed here (e.g. untargeted metabolomics, label-free quantitative proteomics, etc.).

Private (for-profit) clients

Fees are double those listed above, for private sector clients.

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