Child ; Humans ; Proteomics ; methods

Chromatography is a basic process in the current proteomics workflow, and the retention time alignment of the chromatogram is one of the important steps to effectively improve the identification and quantification accuracy. After years of development, a series of algorithms for retention time alignment have been developed. This review summarizes the advances of chromatographic retention time alignment algorithms and tools for proteomics analysis from the perspective of proteomics users, and discusses the development and future application directions.
Algorithms ; Proteomics/methods*

Fatty Liver ; Humans ; Proteomics ; methods

Humans ; Medicine, Chinese Traditional ; Proteomics ; methods

Nowadays, proteomics focuses on quantitative analysis rather than qualitative. In the field of quantitative proteomics, Isobaric tags for relative and absolute quantitation (iTRAQ) is one of the most widely used techniques. The advantage of iTRAQ is high throughput, high stability and free of the restriction of sample property. iTRAQ is suitable for almost all kinds of samples, and up to 8 samples can be analyzed simultaneously by commercially available kit. Along with the development of techniques, more and more mass spectrometry (MS) platforms are used in iTRAQ experiments and the accuracy of iTRAQ has been improved. iTRAQ has been applied to studies of microorganism, animal, plant, medical and protein post-translational modification. Here we review the recent progress in the development of iTRAQ and its applications in quantitative proteomics.
Animals ; Humans ; Mass Spectrometry ; Proteomics ; methods

Electrophoresis, Gel, Two-Dimensional ; methods ; Humans ; Proteomics ; methods ; Urinalysis ; methods

With technological advances in high-throughput sequencing, high resolution mass-spectrometry, and multi-omics data integrative tools and data repositories, the omics research in life sciences are evolving from single-omics strategy to multi-omics strategy. The research of system biology driven by multi-omics will bring a new paradigm in life sciences. This paper briefly summarizes the development of genomics, epigenomics, transcriptomics, proteomics and metabolomics, highlights the composition and function of multi-omics platforms as well as the applications of multi-omics technology, and prospects future applications of multi-omics in synthetic biology and biomedicine.
Genomics ; Proteomics/methods* ; Metabolomics/methods* ; Epigenomics/methods* ; Technology

Amine-specific isobaric tagging (iTRAQ) reagents, as a new class of isobaric reagent, were developed in 2004, which, combined with liquid chromatography and tandem mass spectrometry (LC-MS/MS) , have been applied to the identification and quantification of proteins in a wide range of biological samples, including bacteria, yeasts, human tissues, cells, and fluids. As a new method of quantitative proteomics, the technique of iTRAQ allows for the quantitative analysis of four samples simultaneously and displays its advantages of high-flux, food reproducibility, and high sensitivity; it also provides a potential technological platform for studying the mechanisms of the development and progression of prostate cancer.
Humans ; Isotope Labeling ; methods ; Male ; Prostatic Neoplasms ; metabolism ; Proteomics ; methods

Metaproteomics is an emerging proteomics technology to analyze large scale protein expression in environmental microbial ecosystem. It is termed as the large-scale characterization of the entire protein complement of environmental microbial community at a given point in time. This review focuses on the research strategies and the recent applications in this field based on the published reports and in combination with our own research experiences.
Bacterial Physiological Phenomena ; Ecology ; methods ; Environmental Microbiology ; Proteomics ; methods

Humans ; Proteomics ; methods ; Silicosis ; metabolism ; Specimen Handling ; methods