Test dataset for Quanti workflow.'

Sample Description
218 blood plasma samples from the Kuopio cohort were pooled according to gender and the stage of Alzheimer’s disease (AD) (Control; Stable Mild Cognitive Impairment (S-MCI); Progressive Mild Cognitive Impairment (P-MCI); AD). Each pooled sample was independently digested in triplicate by trypsin in ProteaseMAX™ Surfactant, Trypsin Enhancer (Promega) according to the protocol provided by the producer.
Each peptide digest of pooled samples was analyzed twice using nanoflow C18 reverse phase liquid chromatography (HPLC) (Easy-nLC, Proxeon) with a 60 min gradient coupled with ETD MS/MS on a Velos Orbitrap mass spectrometer (Thermo Fisher Scientific). Survey MS scans were carried out in the Orbitrap Fourier transform mass analyzer with a resolution of 60,000, with the m/z ranging from 300 to 2,000. After each MS scan, the top five most abundant precursor ions were selected for MS/MS using high-energy collision dissociation (HCD) in the Orbitrap (resolution of 7,500) and ETD in the Velos ion trap.

Pooled sample - healthy control males:
Pooled sample - S-MCI males:
Pooled sample - P-MCI males:
Pooled sample - AD males:
Pooled sample - healthy control females:
Pooled sample - S-MCI females:
Pooled sample - P-MCI females:
Pooled sample - AD females:

Related publications
Provided dataset has been used in following publications:

Prognostic polypeptide blood plasma biomarkers of Alzheimer's disease progression(external link). Yang H, Lyutvinskiy Y, Herukka SK, Soininen H, Rutishauser D, Zubarev RA. J Alzheimers Dis. 2014 Jan 1;40(3):659-66. doi: 10.3233/JAD-132102.

In silico instrumental response correction improves precision of label-free proteomics and accuracy of proteomics-based predictive models(external link). Lyutvinskiy Y, Yang H, Rutishauser D, Zubarev RA. Mol Cell Proteomics. 2013 Aug;12(8):2324-31. doi: 10.1074/mcp.O112.023804. Epub 2013 Apr 15.

Alzheimer's disease and mild cognitive impairment are associated with elevated levels of isoaspartyl residues in blood plasma proteins.(external link)
Yang H, Lyutvinskiy Y, Soininen H, Zubarev RA. J Alzheimers Dis. 2011;27(1):113-8. doi: 10.3233/JAD-2011-110626.