Protein Identification

Simple or complex mixtures in solution or gel. Includes reduction, alkylation, digestion, C18 clean up. *Number of proteins identified from 2ug Hela cell lysate on the Lumos MS.Prices for Orbitrap Elite ETD MS or Orbitrap Fusion Lumos ETD/UVPD MS

· LC-MS/MS 60 min gradient. >2,000*

Elite: $130; Lumos: $230

· LC-MS/MS 120 min gradient. >3,000*

Elite: $190; Lumos: $290

· LC-MS/MS 180 min gradient. >3,500*

Elite: $250; Lumos: $350

MW Determination by Direct Infusion (Nanomate)

$50/sample

Single Protein Characterization

Includes reduction, alkylation, digestion, C18 clean up of protein in solution or gel.

· Identification of Post-Translational Modifications (180 min gradient)

Elite: $350; Lumos: $450/sample

· Relative Quantitation of Post-Translational Modifications (180 min gradient)

2 conditions x 3 replicates

Elite: $1,700; Lumos: $2,300

· Phosphopeptide enrichment and identification (180 min gradient)

Elite: $400; Lumos: $500/sample

·De NovoSequencing/Extensive Inspection of Tandem Mass Spectra

$50/hr

Quantitative Proteomics (Unbiased, Discovery Proteomics)

Includes protein assay, reduction/alkylation, digestion, fractionation and or enrichment, quantitative LC-MS/MS, statistical analysis, and preliminary volcano plots and/or heat maps. The number of replicates, fractions, and LC gradient length can be adjusted.

Differential Protein Expression or Abundance Example pricing for projects:

· Label Free Proteomics. 60 min gradient: $230 per sample + $250 for data processing ~500 proteins quantified

2 conditions x 3 biological replicates

Elite: $640; Lumos: $940.

· Label Free Proteomics. 120 min gradient: $290 per sample + $250 for data processing (Recommended for protein interaction and affinity enrichment studies)

2 conditions x 3 biological replicates

Lumos: $1,990

· Label Free Proteomics. 180 min gradient: $350 per sample + $250 for data processing (Recommended for most studies including sorted cells) ~2000-4000 proteins quantified

2 conditions x 5 biological replicates

Lumos: $3,750

· TMT10 plex. Includes reagents, labeling, bRP-LC separation into 12 fractions. 12 x 180 min gradient >6,000 proteins quantified

2 conditions x 5 biological replicates

Lumos: $6,600

Inquire for TMT11, TMT16 or iodoTMT

· SILAC. bRP-LC fractionation into 12 fractions, 12 x 180 min gradient (Does not include media or labeled amino acids)

2 conditions x 1 biological replicate

Elite: $3,200/Biological replicate

Lumos: $4,400/ Biological replicate

Identification of Differentially Regulated Sites of Post-Translational Modification

· TMT10plex (e.g. phosphoproteomics) Includes reagents, labeling, bRP-LC separation into 12 fractions, TiO2or affinity enrichment, 12 x 180 min gradient.

2 conditions x 5 biological replicates

Lumos: $9,069

(Does not include antibody)

· SILAC (e.g. phosphoproteomics) Includes SCX or bRP-LC separation into 12 fractions, TiO2or affinity enrichment, and 12 x 180 min gradient

2 conditions x 1 biological replicate

Lumos: $4,950/Biological Replicate (Does not include media, amino acids, or antibody)

· Label free quantitation or analysis of other PTMs: O-GlcNAc, S-glutathionylation, ubiquitin, fucosylation, glycosylation, acetyl

Please inquire regarding feasibility and cost of enrichment reagents

Targeted Proteomics

2-3 heavy labeled synthetic peptides recommended per protein. Prices for Xevo TQ-S. For projects necessitating higher sensitivity inquire for prices and availability on the Lumos.

· MRM method development

Please inquire

· MRM assay, 30 min gradient

$100/sample

· MRM assay, 60 min gradient

$150/sample

· MRM assay, 90 min gradient

$175/sample

· MRM data analysis (Skyline)

$50/hour

Manual inspection, de novo sequencing, and labeling of MS/MS spectra

$50/hr

Off-line preparative HPLC (strong cation exchange (SCX), high pH C18 reversed phase chromatography (bRP-LC))

$50/hr

New method development/optimization/extensive data processing

$50/hr

For discovery proteomics, LC-MS/MS based services are currently provided using an Ultimate 3000 nano-LC in-line with an Orbitrap Elite ETD MS (ThermoScientific) or an Easy-nLC 1200 in-line with an Orbitrap Fusion Lumos MS.

Identification of peptides is based on a threshold of false discovery rate (FDR) < 0.01="" when="" searching="" a="" forward="" and="" reversed,="" fully="" tryptic="" protein="" database.="" generally="" peptides,="" modified="" peptides,="" and="" protein="" groups="" are="" identified="" with="" maxquant="" using="" fdr="" thresholds="" of="">< 0.01="" at="" the="" psm,="" peptide,="" and="" protein="" level.="" sites="" of="" modification="" target="" proteins="" of="" interest="" are="" manually="" verified.="" for="" global="" studies,="" class="" i="" sites="" of="" modification="" with="" probability="" of="" site="" localization="" of="">75% are reported. Label free quantitation and normalization, performed with the MaxQuant LFQ algorithm, is based on chromatographically resolved peak intensities rather than spectral counting. Other search algorithms are used as needed (Protein Prospector, BioPharmaFinder, Byonic, Skyline, Proteome Discoverer with SEQUEST HT and Mascot). Normalized protein intensities are reported with fold changes and Student’s t test or ANOVA-derived p values adjusted for multiple hypothesis testing (q values). Statistical tests vary with the quantitative approach and experimental design. Reports include preliminary volcano plots and/or heatmaps. Raw data are archived off site. For publication purposes and to comply with NIH data sharing policies, proteomics data are submitted to ProteomeXchange upon request.