SpotLight Proteomics: uncovering the hidden blood proteome improves diagnostic power of proteomics.
The human blood proteome is frequently assessed by protein abundance profiling using a combination of liquid chromatography and tandem mass spectrometry (LC-MS/MS). In traditional sequence database search, many good-quality MS/MS data remain unassigned. Here we uncover the hidden part of the blood proteome via novel SpotLight approach. This method combines de novo MS/MS sequencing of enriched antibodies and co-extracted proteins with subsequent label-free quantification of new and known peptides in both enriched and unfractionated samples. In a pilot study on differentiating early stages of Alzheimer's disease (AD) from Dementia with Lewy Bodies (DLB), on peptide level the hidden proteome contributed almost as much information to patient stratification as the apparent proteome. Intriguingly, many of the new peptide sequences are attributable to antibody variable regions, and are potentially indicative of disease etiology. When the hidden and apparent proteomes are combined, the accuracy of differentiating AD (n = 97) and DLB (n = 47) increased from ≈85% to ≈95%. The low added burden of SpotLight proteome analysis makes it attractive for use in clinical settings.
Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
Susanna L
SL
Lundström
Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
Bo
B
Zhang
Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
Dorothea
D
Rutishauser
Alzheimer's Disease Research Centre, Department of Neurobiology, Care Sciences and, Society, Karolinska Institutet, Stockholm, Sweden.|Centre for Age-related diseases, Stavanger University Hospital, Stavanger, Norway.|Department of Old Age Psychiatry, Institute of Psychiatry, Psychology &Neuroscience, King's College London, London, United Kingdom.
Dag
D
Aarsland
Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
Roman A
RA
Zubarev
D000368:Aged; D000544:Alzheimer Disease / Q000097:blood / Q000175:diagnosis*; D001798:Blood Proteins / Q000378:metabolism*; D003704:Dementia / Q000097:blood / Q000175:diagnosis*; D005260:Female; D006801:Humans; D020961:Lewy Body Disease / Q000097:blood / Q000175:diagnosis*; D008297:Male; D010865:Pilot Projects; D020543:Proteome / Q000378:metabolism*; D040901:Proteomics / Q000379:methods*
D001798:Blood Proteins; D020543:Proteome