Temporal profiles of plasma proteome during childhood development

Abstract

Human blood plasma proteome reflects physiological changes associated with a child’s development as well as development of disease states. While age-specific normative values are available for proteins routinely measured in clinical practice, there is paucity of comprehensive longitudinal data regarding changes in human plasma proteome during childhood. We applied TMT-10plex isobaric labeling-based quantitative proteomics to longitudinally profile the plasma proteome in 10 healthy children during their development, each with 9 serial time points from 9 months to 15 years of age. In total, 1828 protein groups were identified at peptide and protein level false discovery rate of 1% and with at least two razor and unique peptides. The longitudinal expression profiles of 1747 protein groups were statistically modeled and their temporal changes were categorized into 7 different patterns. The patterns and relative abundance of proteins obtained by LC-MS were also verified with ELISA. To our knowledge, this study represents the most comprehensive longitudinal profiling of human plasma proteome to date. The temporal profiles of plasma proteome obtained in this study provide a comprehensive resource and reference for biomarker studies in childhood diseases.

Analysis of the plasma proteome using iTRAQ and TMT‐based Isobaric labeling

“…Without re‐analyzing all these data with unified metrics, an accurate estimation of the relative success of these experiments is difficult. Notably, for example, in accompaniment to their recent TMT study of the maturing proteome, Liu et al re‐analyzed Keshishian's data and stated that the breadth of the proteomic coverage was somewhat less, indicating that using their own parameters the extent of high confidence quantitative data was in the order of 1500–2500 proteins . From their own 10‐plex TMT data they reported 1800 proteins, with in the order of 1000 proteins detected in all reporter channels of their ten 10‐plex TMT experiments.…”

“…For example, in many of the latter day applications, amounting to 35 out of 210 proteins (≥2 unique peptides), or presently in the order of hundreds of proteins and in instances with larger identification lists. As most frequently these have been cross sectional comparisons, that is, of a specific disease state versus control, it is noteworthy that in the analysis of the serum proteome in maturing children (∼1‐15 years of age), Liu et al observed temporal profiles for 900 hundred proteins, underlining the importance of selecting suitable matched controls when comparing subjects.…”

“…It should also be noted that since the representative peptides of each protein are often considered to represent a single entity that the details of potentially important proteoforms should not be overlooked . Furthermore, the importance of lower abundant proteins may become more apparent as increasingly plasma protein lists grow from hundreds to thousands …”

Isobaric Labeling-Based LC-MS/MS Strategy for Comprehensive Profiling of Human Pancreatic Tissue Proteome

“…In the case of more than 10 samples to be compared, multiple TMT experiments will need to be performed, typically with a pooled sample serve as the common reference. (6)…”

“…In addition, the multiplexing capability of isobaric labeling enables an increased analysis throughput, for instance, 10 samples can be analyzed simultaneously using tandem mass tag (TMT)-10plex-based peptide level labeling strategy. (1, 4-6) Furthermore, as missing value issues are common in label free proteomics, TMT10-plex strategy has the advantage of much less missing values due to the co-isolation and fragmentation of the isobaric precursor ions, which provides high quality data for statistical analysis and in turn better statistical power to identify the differentially expressed proteins from the limited number of clinical samples.…”