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We perform state-of-the-art untargeted "shotgun" (discovery-mode) proteomic analyses, as well as targeted MRM-based assays (Go to our Available MRM Assays page).

Contact Us (tlorentz@fredhutch.org)


Typical Untargeted ("Shotgun" LC-MS/MS) Proteomics Results

TMT 10 plex Work Flows Mass / sample (ug) # MS runs MS time (days) global peptides global proteins PO4 sites pY sites
Global 20 24 3 75k-90k 7.1k-7.6k    
Global + deep PO4 500 36 4.5 75k-90k 7.1k-7.6k 10k-21k  
Global + deep PO4 + pY 500 37 4.6 75k-90k 7.1k-7.6k 10k-21k 500-600
Global + 1 step PO4 100 25 3.1 75k-90k 7.1k-7.6k  3-6k  
deep PO4 500 12 1.5 NA NA 10k-21k  
deep PO4 + pY 500 13 1.6 NA NA 10k-21k 500-600
1 Step PO4 (done in triplicate) 75 3 0.4 NA NA  3-6k  

 

Typical Specimen Yields

Biospecimen Estimated protein yield
HeLa cell line 200 µg / 106 cells
MCF10A cell line 300 µg / 106 cells
HMEC line 200 µg / 106 cells
SKBR3 cell line 200 µg / 106 cells 
MDA-MB-361 cell line 160 µg / 106 cells
MDA-MB-468 cell line 220 µg / 106 cells
BT474 cell line 350 µg / 106 cells
HCC1954 cell line 300 µg / 106 cells
lymphoblast cell line (LBL) 100 µg / 106 cells
PBMC (Ficoll preparation) 65 µg protein / 106 cells (~1mL whole blood)
PBMC (expanded in culture) 25 µg / 106 cells
AML blasts  18 µg / 106 cells 
Frozen tumor biopsy (approximate size of a pencil eraser)  1-2 mg
Frozen tumor biopsy (approximate size of a wet grain of rice) 300-500 ug
Breast tumor tissue (fresh frozen) 20-50 µg /mg wet wt. input (2.0-5.0% yield) 
Ovarian tumor tissue (fresh frozen)  25-45 µg /mg wet wt. input (2.5-4.5% yield)  
Pediatric brain tumor tissue (fresh frozen) 30-65 µg /mg wet wt. input (3.0-6.5% yield) 
Brain tumor tissue (fresh frozen) 50-70 µg /mg wet wt. input (5.0-7.0% yield)
Endometrium / Uterine tumor tissue (fresh frozen) 45-75 µg /mg wet wt. input (4.5-7.5% yield)
Head and Neck tumor tissue (fresh frozen) 20-70 µg /mg wet wt. input (2.0-7.0% yield)
Kidney tumor tissue (fresh frozen) 35-70 µg /mg wet wt. input (3.5-7.0% yield)
Lung-Adeno tumor tissue (fresh frozen) 40-65 µg /mg wet wt. input (4.0-6.5% yield)
Lung-Squamous tumor tissue (fresh frozen) 40-70 µg /mg wet wt. input (4.0-7.0% yield)
Pancreas tumor tissue (fresh frozen) 30-40 µg /mg wet wt. input (3.0-4.0% yield)
Soft Tissue / Sarcoma tumor tissue (fresh frozen) 30-45 µg /mg wet wt. input (3.0-4.5% yield)
FFPE section (1cm x 1cm x 10µm) 10-50 µg 
Lymph node FFPE (5µm section)  13-68 µg  
Laser Capture Microdissected tissue 3-5 µg / 10,000 cells 
Core Needle Biopsy    (16G x 1 cm) 100-200 µg
Core Needle Biopsy    (18G x 1 cm) 50-100 µg
Core Needle Biopsy    (20G x 1 cm) 30-60 µg
Core Needle Biopsy    (21G x 1 cm) 20-40 µg