Quantitative Mass Spectrometry Analysis Using PAcIFIC for the Identification of Plasma Diagnostic Biomarkers for Abdominal Aortic Aneurysm

Abstract

BackgroundAbdominal aortic aneurysm (AAA) is characterized by increased aortic vessel wall diameter (>1.5 times normal) and loss of parallelism. This disease is responsible for 1–4% mortality occurring on rupture in males older than 65 years. Due to its asymptomatic nature, proteomic techniques were used to search for diagnostic biomarkers that might allow surgical intervention under nonlife threatening conditions.Methodology/Principal FindingsPooled human plasma samples of 17 AAA and 17 control patients were depleted of the most abundant proteins and compared using a data-independent shotgun proteomic strategy, Precursor Acquisition Independent From Ion Count (PAcIFIC), combined with spectral counting and isobaric tandem mass tags. Both quantitative methods collectively identified 80 proteins as statistically differentially abundant between AAA and control patients. Among differentially abundant proteins, a subgroup of 19 was selected according to Gene Ontology classification and implication in AAA for verification by Western blot (WB) in the same 34 individual plasma samples that comprised the pools. From the 19 proteins, 12 were detected by WB. Five of them were verified to be differentially up-regulated in individual plasma of AAA patients: adiponectin, extracellular superoxide dismutase, protein AMBP, kallistatin and carboxypeptidase B2.Conclusions/SignificancePlasma depletion of high abundance proteins combined with quantitative PAcIFIC analysis offered an efficient and sensitive tool for the screening of new potential biomarkers of AAA. However, WB analysis to verify the 19 PAcIFIC identified proteins of interest proved inconclusive save for five proteins. We discuss these five in terms of their potential relevance as biological markers for use in AAA screening of population at risk.

Using Proteomics to Understand Abdominal Aortic Aneurysms: Where Are We?

“…Moreover, in Figure 3, we reported the percentage of proteins identified by each author. This analysis pointed out that Acosta-Martin et al [29] identified about 77% of plasma proteins. This high percentage of identification is probably due to the use of the dataindependent shotgun proteomic strategy PAcIFIC [29].…”

“…Acosta-Martin et al [29], using a data-independent shotgun proteomic strategy called Precursor Acquisition Independent From Ion Count (PAcIFIC), combined with spectral counting and isobaric tandem mass tags, identified 80 proteins as statistically differentially abundant between AAA and control patients. They used pooled human plasma samples of AAA and control patients depleted of the most abundant proteins.…”

“…They used pooled human plasma samples of AAA and control patients depleted of the most abundant proteins. Among differentially abundant proteins, five of them were verified to be differentially up-regulated in plasma of AAA patients: adiponectin, extracellular superoxide dismutase, protein AMBP, kallistatin and carboxypeptidase B2 [29]. Several highthroughput multiplexed techniques have been recently developed to assess protein expression at a functional level.…”

“…Ig alpha-1 chain C region IGHA1_HUMAN [18,25,29] several authors suggesting the idea of their possible role in the AAA development. Then, we listed the proteins, identified by more than one author, in Table 3.…”

Mass spectrometry-based proteomics and peptidomics for systems biology and biomarker discovery

“…In addition, the tissue of origin for the identified plasma proteins were identified and its origin was more diverse as the protein concentration decreased (Zhang et al, 2011c). Plasma has been used as a source for biomarker studies such as colorectal cancer Murakoshi et al, 2011), cardiovascular disease (Addona et al, 2011), and abdominal aortic aneurysm (Acosta-Martin et al, 2011). Even though the blood brain barrier prevents direct blood to brain interaction, neurological disorders, such as Alzheimer's disease (AD), have had their proteomes studied using plasma (Ray et al, 2007).…”