Data-independent acquisition (DIA) is a high-throughput, unbiased mass spectrometry data acquisition method which has good quantitative reproducibility and is friendly to low-abundance proteins. It becomes the preferred choice for clinical proteomic studies especially for large cohort studies in recent years. The mass-spectrometry (MS)/MS spectra generated by DIA is usually heavily mixed with fragment ion information of multiple peptides, which makes the protein identification and quantification more difficult. Currently, DIA data analysis methods fall into two main categories, namely peptide-centric and spectrum-centric. The peptide-centric strategy is more sensitive for identification and more accurate for quantification. Thus, it has become the mainstream strategy for DIA data analysis, which includes four key steps: building a spectral library, extracting ion chromatogram, feature scoring and statistical quality control. This work reviews the peptide-centric DIA data analysis procedure, introduces the corresponding algorithms and software tools, and summarizes the improvements for the existing algorithms. Finally, the future development directions are discussed.
Humans ; Proteomics/methods* ; Reproducibility of Results ; Peptides/chemistry* ; Software ; Algorithms ; Tandem Mass Spectrometry/methods* ; Proteome/analysis*

Schizophrenia is a severe psychiatric disorder with an unclear etiology and various clinical manifestations. The diagnosis and consequent treatment of schizophrenia mainly rely on clinical symptoms. Multiple risk sites associated with schizophrenia have been identified, yet objective indicators have not been found to facilitate clinical diagnosis and treatment of schizophrenia. The development of omics technology provides different perspectives on the etiology of schizophrenia and make the early identification, diagnosis and treatment of the disorder possible. This article summarizes the prevalence of schizophrenia, reviews the research results and shortcomings of transcriptomics and proteomics, as well as the latest achievements and prospects of multi-omics, aiming to reveal the use of omics in SZ, provide more comprehensive biological evidence to reveal the complex pathogenesis of schizophrenia and provide a theoretical basis for the early identification, accurate diagnosis, disease progression control, and prognosis improvement of schizophrenia.
Humans ; Proteomics/methods* ; Transcriptome ; Schizophrenia/genetics*

OBJECTIVES: To study the changes of protein levels in peripheral blood after it dried. METHODS: The proteins from whole blood and bloodstains were detected by liquid chromatography-tandem mass spectrometry (LC-MS/MS) and normalized by the label-free quantification (LFQ) method. The differential proteins were analyzed by using R 4.2.1 software, limma and edgeR package. The analysis of biological function, signaling pathway and subcellular localization for the differential proteins was then performed. RESULTS: A total of 623 and 596 proteins were detected in whole blood and bloodstains, respectively, of which 31 were statistically significant in the quantitative results, including 10 up-regulated and 21 down-regulated proteins in bloodstains. CONCLUSIONS The protein abundances in whole blood and bloodstains are highly correlated, and the variation of protein abundances may be related to the changes of endogenous and structural proteins in cells. The application of proteomics technology can assist the screening and identification of protein biomarkers, thereby introducing new biomarkers for forensic research.
Chromatography, Liquid/methods* ; Tandem Mass Spectrometry/methods* ; Proteomics/methods* ; Blood Stains ; Biomarkers

Schizophrenia is a severe psychiatric disorder with an unclear etiology and various clinical manifestations. The diagnosis and consequent treatment of schizophrenia mainly rely on clinical symptoms. Multiple risk sites associated with schizophrenia have been identified, yet objective indicators have not been found to facilitate clinical diagnosis and treatment of schizophrenia. The development of omics technology provides different perspectives on the etiology of schizophrenia and make the early identification, diagnosis and treatment of the disorder possible. This article summarizes the prevalence of schizophrenia, reviews the research results and shortcomings of transcriptomics and proteomics, as well as the latest achievements and prospects of multi-omics, aiming to reveal the use of omics in SZ, provide more comprehensive biological evidence to reveal the complex pathogenesis of schizophrenia and provide a theoretical basis for the early identification, accurate diagnosis, disease progression control, and prognosis improvement of schizophrenia.
Humans ; Proteomics/methods* ; Transcriptome ; Schizophrenia/genetics*

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

The systematic and in-depth study of phosphoproteome rely on highly reproducible and specific phosphopeptide enrichment methods. At present, a variety of enrichment methods have been developed based on different principles, and these methods often display different selectivity and specificity. It is therefore very important to select the most suitable enrichment method according to different research purposes. This review summarized the phosphopeptide enrichment based on affinity chromatography, immunoprecipitation, chemical derivatization, chromatography and other newly developed methods. The advantages and disadvantages of these methods, as well as the related optimization and improvement strategies, were discussed in detail. In addition, we also briefly summarized the progress of the combination of phosphopeptide enrichment and fractionation methods developed in recent years.
Phosphopeptides/metabolism* ; Proteomics/methods* ; Titanium/chemistry* ; Chromatography, Affinity ; Proteome ; Phosphorylation

Metabolomics, which mainly studies the metabolite components of organisms, tissues, cells and their dynamic changes, is an emerging omics technology following genomics and proteomics. Metabolites are the final products of cellular regulation, and the concentration of metabolites is considered to be the ultimate response of a biological system to genetic or environmental changes. Secondary metabolites with chemical diversity are widely present in living organisms, thus accurate quantification of secondary metabolites through appropriate analytical platforms is an important task of metabolomics. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) is the most commonly used method for the detection of metabolites, providing a basis for the wide application of plant secondary metabolites. This review summarizes the advances of using LC-MS/MS techniques for the detection of phytohormone, folic acid, flavonoids and other secondary metabolites.
Chromatography, Liquid/methods* ; Tandem Mass Spectrometry/methods* ; Metabolomics/methods* ; Plants ; Proteomics

The purpose of this study was to explore the effect of acute hypoxia on urine proteome in rats. In this study, rats were placed in a hypoxic chamber simulating a plateau environment at an altitude of 5 000 m for 24 hours. Urine samples were collected at 0, 12, and 24 h after hypoxia. Urinary proteins were profiled using liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS). Compared with the control (before hypoxia), a total of 144 differentially expressed proteins were identified in the hypoxia 12 h group, and 129 differentially expressed proteins were identified in the hypoxia 24 h group. Functional annotation analysis revealed that these differentially expressed proteins were involved in a series of biological pathways related to hypoxic stress, such as anti-oxidative stress, glycolysis, complement and coagulation cascade. Our results suggest that the urinary proteome can reflect significant changes upon acute hypoxic stimulation. These findings may provide an approach to judge the hypoxia state of the body and help to assist the detection of hypoxia state.
Animals ; Rats ; Proteome/analysis* ; Chromatography, Liquid/methods* ; Tandem Mass Spectrometry/methods* ; Proteomics/methods* ; Hypoxia

Type 2 diabetes mellitus (T2DM) is a global metabolic disease with potentially life- threatening complications. Liver metabolism plays a vital role in the occurrence and development of diabetes mellitus. It has been reported that the Chinese medicinal Anemarrhenae rhizoma (AR) can relieve insulin resistance and diabetes mellitus. However, the effect on abnormal liver metabolism in diabetes mellitus is still unclear. Therefore, we extracted liver proteins of T2DM rats induced by high-fat diet (HFD) and streptozotocin (STZ), T2DM rats treated with AR extract (ARE), obesity rats (fed with HFD), and normal control rats (fed with normal diet). Then, through tandem mass tag (TMT) labeling combined with mass spectrometry (MS), we obtained the quantitative proteomic data. Bioinformatics software was used for hierarchical cluster analysis and principal component analysis of the data in each group. The volcano map for differentially expressed proteins (P < 0.05, fold change > 1.5) was plotted. It was found that the treatment group was closer to the normal control group, indicating that the quantitative proteomic data of liver tissue can reflect the therapeutic effect of ARE on T2DM rats. Key protein clusters closely related to the treatment of ARE were screened out. The Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways of the protein clusters were analyzed by David, and the result showed that AR's alleviation of abnormal fatty acid metabolism in livers of T2DM rats may be related to the regulation of the expression of key proteins Ndufa6 and Prkar2b.
Rats ; Animals ; Diabetes Mellitus, Type 2/metabolism* ; Proteomics/methods* ; Drugs, Chinese Herbal/therapeutic use* ; Anemarrhena ; Liver/metabolism*

The purpose of this study was to understand the effect of gender on the traits of wool. One-year-old male and female Chinese merino sheep (JunKen type) were used to screen differentially expressed proteins in skin tissues by quantitative proteomics using liquid chromatography-tandem mass spectrometry (LC-MS/MS) and data independent acquisition (DIA) strategy. This was followed by GO function annotation, KEGG metabolic pathway and protein network interaction analysis on the differential proteins obtained. The result showed that there were 674 differentially expressed proteins between male and female groups, whereas 280 proteins were up-regulated and 394 proteins were down-regulated in the male group. Through further comparison and analysis, there were 43 differentially expressed proteins related to skin hair follicle development and wool phenotype, 30 up-regulated and 13 down-regulated. The GO annotation analysis of differentially expressed proteins were mainly enriched in 37 processes of molecular function such as oxygen binding, chondroitin sulfate binding, heme binding, glutathione peroxidase activity and glutathione transferase activity; 120 biological processes such as cellular oxidant detoxification, regulation of muscle contraction, notch signaling pathway, calcium ion transmembrane transport and glutathione metabolism; and 31 processes related to cellular components such as mast cell granule, nucleus, sarcoplasmic reticulum and endoplasmic reticulum lumen. KEGG analysis showed that the differentially expressed proteins were involved sixteen signaling pathways, among which MAPK and p53 signaling pathways were closely related to wool growth and development. The protein network interaction analysis discovered that COL1A1 was closely related to MMP2, SPARC, THBS1 and other differentially expressed proteins, which might play a key role in wool growth and development. Thus, this study obtained basic data for revealing the molecular mechanism of sheep wool traits of different gender.
Animals ; Male ; Female ; Proteomics ; Chromatography, Liquid/methods* ; Tandem Mass Spectrometry/methods* ; Wool ; China