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Fig. 6 | Clinical Proteomics

Fig. 6

From: Optimized sample preparation and data analysis for TMT proteomic analysis of cerebrospinal fluid applied to the identification of Alzheimer’s disease biomarkers

Fig. 6

Comparison of the sample preparation techniques (1) in-solution digestion and (2) filter-assisted sample preparation (FASP). Five replicate CSF pool samples were prepared with in-solution digestion protocol and FASP each. LC–MS analysis was performed separately for both sets of replicates. Following quantification, the number of peptides identified employing FASP and in-solution digestion were determined (A). Likewise, the amount of identified proteins with both approaches was evaluated (B). To assess contamination, the number of peptides derived from keratins was calculated for the two preparation techniques (C). Log2-transformed reporter ion intensities (RII) of peptide group abundances were plotted for all TMT channels (in-solution and FASP) for evaluation of yield and reproducibility (D)

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