The human plasma proteome: Analysis of Chinese serum using shotgun strategy

Abstract

We have investigated the serum proteome of Han-nationality Chinese by using shotgun strategy. A complete proteomics analysis was performed on two reference specimens from a total of 20 healthy donors, in which each sample was made from ten-pooled male or female serum, respectively. The methodology used encompassed (1) removal of six high-abundant proteins; (2) tryptic digestion of low- and high-abundant proteins of serum; (3) separation of peptide mixture by RP-HPLC followed by ESI-MS/MS identification. A total of 944 nonredundant proteins were identified under a stringent filter condition (X(corr) > or = 1.9, > or = 2.2, and > or = 3.75, < or = C(n) > or = 0.1, and R(sp) > or = 4.0) in both pooled male and female samples, in which 594 and 622 entire proteins were found, respectively. Compared with the total 3020 protein identifications confirmed by more than one laboratory or more than one specimen in HUPO Plasma Proteome Project (PPP) participating laboratories recently, 206 proteins were identified with at least two distinct peptides per protein and 185 proteins were considered as high-confidence identification. Moreover, some lower abundance serum proteins (ng/mL range) were detected, such as complement C5 and CA125, routinely used as an ovarian cancer marker in plasma and serum. The resulting nonredundant list of serum proteins would add significant information to the knowledge base of human plasma proteome and facilitate disease markers discovery.

In-depth research of multidrug resistance related cell surface glycoproteome in gastric cancer

“…The proteins identified by the same peptides were grouped. To remove the redundancy of identifications, only one protein was kept for each group by using the following order as described by He et al [20]. The molecular function and the involved biological process of the identified N-glycoproteins were classified by browsing the PANTHER database [21].…”

Suction blister fluid as potential body fluid for biomarker proteins

“…This reversed database was constructed by using the reversed order of amino acid sequences of every protein in a similar way as described by Peng et al, Kislinger et al, and Moore et al [28][29][30]. Although, we realize that this analysis if far from comprehensive, we note that comparable numbers of proteins were found in previous 2-D-HPLC MS/MS proteome analyses on human serum, when similarly high database search stringencies were used [26,[31][32][33]. In these studies, the amounts of serum proteins ranged from 325 to 622.…”

Human body fluid proteome analysis

“…Interpretation of the listed data should be cautious considering different criteria and algorithms might be used for database searching and assigning protein IDs. A simple shotgun experiment based on 1-D or 2-D LC-MS/MS typically yields a list of a few hundred distinct proteins [31][32][33][34][35]. Multiplexed proteomics platforms, which often consist of prefractionation, multidimensional separation, and MS/MS techniques, are required in order to achieve a more comprehensive analysis.…”