Individual CSF samples from another set of 10 healthy volunteers, age 37 — 44 years (median = 40) and 5 women and 5 men, were analyzed by LC - MS analysis
without immunoaffinity depletion.
Due to the limit in sample volume, the CSF samples used in individual LC - MS analyses were not
immunoaffinity depleted and fractionated, and therefore had much lower proteome coverage compared to the pooled samples.
Instead of permanently depositing particles
through immunoaffinity, anti-EpCAM coated magnetic microparticles were trapped over the untreated PDMS surface by an external magnetic field and were then released by readily removing the magnet for CTC collection.
The group
uses immunoaffinity — the specific chemical affinity between an antibody and an antigen — to make CTCs adhere to the device while normal blood cells flow past.
Combining immunoaffinity - based partitioning, SCX fractionation and LC - MS / MS, we identified approximately 30,000 peptides for each pooled sample corresponding to 2,783 nonredundant proteins in CFS patient samples and 2,768 proteins in nPTLS patient samples, compared to the 2,630 proteins present in the CSF of healthy normal control subjects.
Individual CSF samples from a group of 14 of the 25 nPTLS subjects (aged 25 — 58 years with a median age of 48 years, 6 female and 8 male) were also used in direct LC - MS analysis
without immunoaffinity depletion.
Individual CSF samples from 14 of the 43 CFS subjects (aged 33 — 48 years with a median age of 43 years, 7 female and 7 male) were also used in direct LC - MS analysis (i.e., no MS / MS was performed) without
immunoaffinity depletion.
The bound fraction of abundant proteins from
the immunoaffinity depleted flow through fraction was analyzed separately and included in the subsequent analysis.