Flow chart of the rostro-caudal gradient study.

<p>In the rostro-caudal gradient (RCG) study, we examined the seven following points of the RCG from a PSP patient: 1-2^nd, 10-11^th, 16-17^th, 24-25^th, 31-32^nd, 38-39^th and 44-45^th mL CSF, referred to as RCG point 1-7, respectively. Twelve samples were digested and iTRAQ labeled (114-117). A reference, (labeled with iTRAQ reagent 114) containing the same amount of each RCG point, was included in each experiment. The RCG points 1 and 7 were included twice. After digestion and iTRAQ-labeling, samples were combined as follows: Exp. 1 (reference, 44-45^th mL, 24-25^th mL and 1-2^nd mL), Exp. 2 (reference, 1-2^nd mL, 38-39^th mL and 16-17^th mL), and Exp. 3 (reference, 10-11^th mL, 44-45^th mL and the 31-32^nd mL). The three experiments were fractionated by mixed mode reversed phase-anion chromatography (MM (RP-AX)) and analyzed on an Orbitrap Velos Pro. The protein abundances were averaged for each protein in the duplicate samples.</p

Protein concentration measurement of along the rostro-caudal gradient.

<p>Protein concentration of the cerebrospinal fluid (CSF)-derived proteins from the seven points along the rostro-caudal gradient (RCG). The CSF was measured in triplicates with Qubit, and error bars of the standard deviation are included. R squared value 0.8931.</p

Categorization of proteins based on fold change, R-squared values and major expected contributing source of origin.

<p>In order to explore how different proteins were affected by the rostro-caudal gradient, we used the fold change and R-squared values of the proteins quantified with SID-MRM and iTRAQ to categorize the proteins into the three categories: affected by the RCG, unaffected by the RCG and uncertain. The fold change was calculated between the 1-2^nd and 44-45^th mL of CSF (referred to as RCG point 1 and 7), and the classification was based on the criteria from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090429#pone-0090429-t001" target="_blank">Table 1</a>.The proteins are also categorized into groups based on the major expected contributing source of origin, with Uniprot as the primary reference unless otherwise stated. See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090429#pone.0090429.s006" target="_blank">Table S5</a> for details. The asterisk (*) marks conflicting results: affected + unaffected  =  uncertain; affected + uncertain  =  affected; unaffected + uncertain  =  unaffected. Proteins only quantified in the SID-MRM study is marked with ^a.</p

Use of Stable Isotope Dimethyl Labeling Coupled to Selected Reaction Monitoring to Enhance Throughput by Multiplexing Relative Quantitation of Targeted Proteins

In this manuscript, we present a proof-of-concept study for targeted relative protein quantitation workflow using chemical labeling in the form of dimethylation, coupled with selected reaction monitoring (dimethyl-SRM). We first demonstrate close to complete isotope incorporation for all peptides tested. The accuracy, reproducibility, and linear dynamic range of quantitation are further assessed based on known ratios of nonhuman standard proteins spiked into human cerebrospinal fluid (CSF) as a model complex matrix. Quantitation reproducibility below 20% (CV < 20%) was obtained for analyte concentrations present at a dynamic range of 4 orders of magnitude lower than that of the background proteins. An error of less than 15% was observed when measuring the abundance of 44 out of 45 major human plasma proteins. Dimethyl-SRM was further examined by comparing the relative quantitation of eight proteins in human CSF with the relative quantitation obtained using synthetic heavy peptides coupled to stable isotope dilution-SRM (SID-SRM). Comparison between the two methods reveals that the correlation between dimethyl-SRM and SID-SRM is within 0.3–33% variation, demonstrating the accuracy of relative quantitation using dimethyl-SRM. Dimethyl labeling coupled with SRM provides a fast, convenient, and cost-effective alternative for relative quantitation of a large number of candidate proteins/peptides

Overview of the conducted studies.

<p>Blood contamination: in experiment A protein depleted CSF was separated by SDS-PAGE, in experiment B crude CSF was in-solution digested. Progenesis LC-MS was used for data analysis. In the rostro-caudal gradient study, we used iTRAQ-labeling with mixed mode reversed phase-anion chromatography (MM (RP-AX)) fractionation. The Spectrum Mill software was used for data analysis. For verification we used stable isotope dilution (SID) multiple reaction monitoring (MRM) to monitor 70 peptides. MM (RP-AX) chromatography was used for fractionation and the MultiQuant software was used for data analysis. In the plasma/CSF ratio study equal amount of corresponding CSF and plasma from five patients were compared using dimethyl labeling. Samples were fractionated using strong cation exchange (SCX) chromatography. Proteome discoverer was used for data analysis. For all discovery experiments the samples were analyzed on an Orbitrap Velos Pro and for SID-MRM the samples were analyzed on a Q-trap 5500. SIS = Stable Isotope Standards</p

Flow chart of the plasma/CSF study.

<p>We compared the cerebrospinal fluid (CSF) and plasma protein ratio of five patients (P1-P5) using dimethyl labeling. The reference sample was a mix of equal total amount of CSF and plasma, and was labeled by light reagents. The five CSF samples were labeled by intermediate (IM) reagents, and the plasma samples were labeled by the heavy reagents. The light, IM and heavy labeled samples were combined and fractionated into eight fractions by strong cation exchange chromatography and analyzed on an Orbitrap Velos Pro. The average (and standard deviation) protein concentration of CSF and plasma, age at sampling and ratio male/female of the five patients are presented in the figure.</p

Use of Stable Isotope Dimethyl Labeling Coupled to Selected Reaction Monitoring to Enhance Throughput by Multiplexing Relative Quantitation of Targeted Proteins

In this manuscript, we present a proof-of-concept study for targeted relative protein quantitation workflow using chemical labeling in the form of dimethylation, coupled with selected reaction monitoring (dimethyl-SRM). We first demonstrate close to complete isotope incorporation for all peptides tested. The accuracy, reproducibility, and linear dynamic range of quantitation are further assessed based on known ratios of nonhuman standard proteins spiked into human cerebrospinal fluid (CSF) as a model complex matrix. Quantitation reproducibility below 20% (CV < 20%) was obtained for analyte concentrations present at a dynamic range of 4 orders of magnitude lower than that of the background proteins. An error of less than 15% was observed when measuring the abundance of 44 out of 45 major human plasma proteins. Dimethyl-SRM was further examined by comparing the relative quantitation of eight proteins in human CSF with the relative quantitation obtained using synthetic heavy peptides coupled to stable isotope dilution-SRM (SID-SRM). Comparison between the two methods reveals that the correlation between dimethyl-SRM and SID-SRM is within 0.3–33% variation, demonstrating the accuracy of relative quantitation using dimethyl-SRM. Dimethyl labeling coupled with SRM provides a fast, convenient, and cost-effective alternative for relative quantitation of a large number of candidate proteins/peptides