Quantification Technology Research Articles

Divergent Proteome Patterns of Egg Albumen from Domestic Chicken, Duck, Goose, Turkey, Quail and Pigeon

To uncover a diversity of genetic and biological unknowns, a comprehensive and comparative proteomic analysis is performed on egg albumen of domestic chicken, duck, goose, turkey, quail, and pigeon with tandem mass tags quantification technology. In this study, a total of 148, 138, 150, 162, 183, and 179 proteins are identified in egg albumen of the above six species, respectively. Venn plots, PCA, and cluster analysis all reveal the highest similarity of protein composition between duck and goose (≈75%). Additionally, the six species have 52 proteins detected in common in the egg albumen. As revealed by GO and pathway analyses, the plausible functions of these highly conserved proteins are to provide a secure environment and prevent the early death of embryonic cells. Species-specific proteins such as haptoglobin in pigeon, serpin-like protein HMSD in duck, and ovodefensin in chicken are also screened and are likely associated with species-dependent biological processes. Furthermore, Enzyme Code analysis indicated egg albumen have abundant enzyme activity, with hydrolases accounting for more than half of the total enzymes. This study is the first to provide the proteome profiles of egg albumen for the major poultry species, which will be instructive for the understanding of species-specific biological problems with egg albumen.

Measurements of the trapezius and erector spinae muscles using virtual touch imaging quantification ultrasound-Elastography: a cross section study

BackgroundThis study uses virtual touch imaging quantification (VTIQ) technology for the first time to conduct measurements of the trapezius and erector spinae muscles in a large study population. The significance of various influencing factors, such as age and sex, are also examined.MethodThe study population comprised 278 subjects. The Siemens Acuson S3000 and VTIQ technology were used for measurements of the trapezius and erector spinae muscles (Siemens Healthcare, Erlangen, Germany).ResultsThe following mean values ± standard deviation were calculated: left trapezius: males 2.89 ± 0.38 m/s, females 2.71 ± 0.37 m/s; right trapezius: males 2.84 ± 0.41 m/s, females 2.70 ± 0.38 m/s; left erector spinae: males 2.97 ± 0.50 m/s, females 2.81 ± 0.57 m/s; right erector spinae: males 3.00 ± 0.52 m/s, females 2.77 ± 0.59 m/s. A significant difference between male and female subjects was demonstrated both for the shear wave velocities of the trapezius and erector spinae as well as for the thickness of the trapezius muscle (p < 0.05). There was also a significant difference in muscle elasticity between subjects over 60 years of age and those under 60 (p < 0.05). Furthermore, the results indicate that regular physical activity has an effect on muscle elasticity.ConclusionsOur results demonstrate significantly different results between male and female subjects and between under- and over-sixty-year-old subjects. This means that sex-related and age-adapted considerations are obviously needed for further studies.

Portable Multispectral Colorimeter for Metallic Ion Detection and Classification.

This work deals with a portable device system applied to detect and classify different metallic ions as proposed and developed, aiming its application for hydrological monitoring systems such as rivers, lakes and groundwater. Considering the system features, a portable colorimetric system was developed by using a multispectral optoelectronic sensor. All the technology of quantification and classification of metallic ions using optoelectronic multispectral sensors was fully integrated in the embedded hardware FPGA ( Field Programmable Gate Array) technology and software based on virtual instrumentation (NI LabView®). The system draws on an indicative colorimeter by using the chromogen reagent of 1-(2-pyridylazo)-2-naphthol (PAN). The results obtained with the signal processing and pattern analysis using the method of the linear discriminant analysis, allows excellent results during detection and classification of Pb(II), Cd(II), Zn(II), Cu(II), Fe(III) and Ni(II) ions, with almost the same level of performance as for those obtained from the Ultravioled and visible (UV-VIS) spectrophotometers of high spectral resolution.

Significant and unique changes in phosphorylation levels of four phosphoproteins in two apple rootstock genotypes under drought stress.

Drought stress is a major problem around the world and there is still little molecular mechanism about how fruit crops deal with moderate drought stress. Here, the physiological and phosphoproteomic responses of drought-sensitive genotype (M26) and drought-tolerant genotype (MBB) under moderate drought stress were investigated. Our results of the physiology analysis indicated that the MBB genotype could produce more osmosis-regulating substances. Furthermore, phosphoproteins from leaves of both genotypes under moderate drought stress were analyzed using the isobaric tags for relative and absolute quantification technology. A total of 595 unique phosphopeptides, 682 phosphorylated sites, and 446 phosphoproteins were quantitatively analyzed in the two genotypes. Five and thirty-five phosphoproteins with the phosphorylation levels significantly changed (PLSC) were identified in M26 and MBB, respectively. Among these, four PLSC phosphoproteins were common to both genotypes, perhaps indicating a partial overlap of the mechanisms to moderate drought stress. Gene ontology analyses revealed that the PLSC phosphoproteins represent a unique combination of metabolism, transcription, translation, and protein processing, suggesting that the response in apple to moderate drought stress encompasses a new and unique homeostasis of major cellular processes. The basic trend was an increase in protein and organic molecules abundance related to drought. These increases were higher in MBB than in M26. Our study is the first to address the phosphoproteome of apple rootstocks in response to moderate drought stress, and provide insights into the molecular regulation mechanisms of apple rootstock under moderate drought stress.

Targeted quantification of functional enzyme dynamics in environmental samples for microbially mediated biogeochemical processes.

Microbial enzymes catalytically drive biogeochemical processes in environments. The dynamic linkage between functional enzymes and biogeochemical species transformation has, however, rarely been investigated for decades because of the challenges to directly quantify enzymes in environmental samples. The diversity of microorganisms, the low amount of available biomass and the complexity of chemical composition in environmental samples represent the main challenges. To address the diversity challenge, we first identify several signature peptides that are conserved in the targeted enzymes with the same functionality across many phylogenetically diverse microorganisms using metagenome-based protein sequence data. Quantification of the signature peptides then allows estimation of the targeted enzyme abundance. To achieve analyses of the requisite sensitivity for complex environmental samples with low available biomass, we adapted a recently developed ultrasensitive targeted quantification technology, termed high-pressure high-resolution separations with intelligent selection and multiplexing (PRISM) by improving peptide separation efficiency and method detection sensitivity. Nitrate reduction dynamics catalyzed by dissimilatory and assimilatory enzymes in a hyporheic zone sediment was used as an example to demonstrate the application of the enzyme quantification approach. Together with the measurements of biogeochemical species, the approach enables investigating the dynamic linkage between functional enzymes and biogeochemical processes.

Clinical utility of single molecule counting technology for quantification of KIM-1 in patients with heart failure and chronic kidney disease

BackgroundAcute kidney injury (AKI) is associated with high morbidity and mortality, and may lead to chronic kidney disease (CKD). Traditional serum biomarkers for acute and chronic renal dysfunction are insensitive and nonspecific. While urinary kidney injury molecule-1 (KIM-1) is a sensitive and specific measure of kidney tubular injury, it is difficult to obtain in acute settings. Thus, our objective was to develop a highly sensitive immunoassay for plasma KIM-1. MethodsA novel plasma KIM-1 immunoassay was developed using Single Molecule Counting technology (SMC). It was clinically validated in: 120 healthy subjects to establish a preliminary reference range; 25 healthy subjects to assess biological variability; 200 patients with heart failure (CHF); and 60 patients from a CKD case control. ResultsSMC KIM-1 assay provided a limit of detection of 1.4pg/mL (reporting range from 2pg/mL to 1000pg/mL). Inter-assay precision was 9–15% CV. Median KIM-1 value in healthy subjects was 119pg/mL with a RR 95th percentile of 292pg/mL. KIM-1 demonstrated low weekly biological variability over 6weeks. KIM-1 was elevated in patients with CKD or CHF. Adjusted odds ratios for differentiating CHF or CKD from controls were 9.6 (95% CI 2.7–35.0) and 3.6 (95% CI 1.1–11.6), respectively. In CHF, KIM-1 values correlated inversely with eGFR (Spearman R=−0.32, p<0.0001). ConclusionsPlasma KIM-1 is quantifiable in healthy volunteers, elevated in CKD and CHF patients, and correlates with eGFR. Additional investigation is needed to determine if KIM-1 provides prognostic value for CKD and CHF patient outcomes.

The correlation between HER-2 expression and the CEUS and ARFI characteristics of breast cancer.

ObjectiveThe purpose of the present study was to explore the correlation between the contrast-enhanced ultrasound (CEUS) and acoustic radiation force impulse (ARFI) characteristics of breast cancers and the expression of human epidermal growth factor receptor 2 (HER-2).MethodsHER-2 expression levels in the tumor masses of 167 clearly diagnosed cases of breast cancer were measured and analyzed. The enhancement features and time intensity curve (TIC) of CEUS and virtual touch tissue imaging (VTI) and virtual touch tissue quantification (VTQ) technology of ARFI were employed to analyze the relationship between HER-2 expression and the CEUS and ARFI characteristics of breast cancer.Results(1) Statistically significant differences in the distribution of the contrast agent, perforator blood flow, the overranging phenomenon and perfusion defects between the study groups with different HER-2 expression levels (P < 0.05) were observed on CEUS. In addition, statistically significant differences in the TIC peak time (PT), slope of the ascending branch (K) and area under the curve (AUC) were found in the groups expressing different levels of HER-2 (P < 0.05). In contrast, the degree of contrast agent enhancement and TIC peak intensity (PI) were found to be independent of the expression status of HER-2, as they were not statistically significant (P > 0.05). (2) Statistically significant differences in the VTQ results between the groups with different HER-2 expression levels were found (P < 0.05). However, no statistically significant differences in VTI image characteristics were detected between the groups expressing different levels of HER-2 (P > 0.05).ConclusionA correlation was found between the CEUS and ARFI characteristics of breast cancer and HER-2 expression levels. This correlation was principally reflected in perfusion defects, perforator blood flow, PI, PT, K and VTQ.

Development of a Multiplexed Liquid Chromatography Multiple-Reaction-Monitoring Mass Spectrometry (LC-MRM/MS) Method for Evaluation of Salivary Proteins as Oral Cancer Biomarkers

Multiple (selected) reaction monitoring (MRM/SRM) of peptides is a growing technology for target protein quantification because it is more robust, precise, accurate, high-throughput, and multiplex-capable than antibody-based techniques. The technique has been applied clinically to the large-scale quantification of multiple target proteins in different types of fluids. However, previous MRM-based studies have placed less focus on sample-preparation workflow and analytical performance in the precise quantification of proteins in saliva, a noninvasively sampled body fluid. In this study, we evaluated the analytical performance of a simple and robust multiple reaction monitoring (MRM)-based targeted proteomics approach incorporating liquid chromatography with mass spectrometry detection (LC-MRM/MS). This platform was used to quantitatively assess the biomarker potential of a group of 56 salivary proteins that have previously been associated with human cancers. To further enhance the development of this technology for assay of salivary samples, we optimized the workflow for salivary protein digestion and evaluated quantification performance, robustness and technical limitations in analyzing clinical samples. Using a clinically well-characterized cohort of two independent clinical sample sets (total n = 119), we quantitatively characterized these protein biomarker candidates in saliva specimens from controls and oral squamous cell carcinoma (OSCC) patients. The results clearly showed a significant elevation of most targeted proteins in saliva samples from OSCC patients compared with controls. Overall, this platform was capable of assaying the most highly multiplexed panel of salivary protein biomarkers, highlighting the clinical utility of MRM in oral cancer biomarker research.

Value of MRI T2* in quantification of visceral iron deposition in patients with β-thalassemia major

Objective To explore the value of MRI T2*quantification of visceral iron deposition in patients with β-thalassemia major. Methods A total of one hundred and two patients with β-thalassemia major were retrospectively analyzed. They underwent genetic testing and the cardiac and (or) abdominal MRI scanning. Among them, 47 patients underwent splenectomy operation, 95 patients underwent cardiac MRI scanning, 102 underwent abdominal MRI scanning for their livers, pancreases and kidneys, and 55 underwent splenic MRI scanning. The T2* values of the hearts, livers, pancreases and kidneys were measured, meanwhile the liver iron concentrations (LIC) were measured. The levels of serum ferritin (SF) patients were measured in 81 patients. The Spearman rank correlation was employed to analyze the relationship between SF, LIC, age and each organs T2* values. Independent sample t test (normal distribution) or the Mann-Whitney U test (non-normal distribution) were used to compare the hepatic, cardiac, renal and splenic T2* values differences between patients with splenectomy and those without. Results Serum ferritin were highly positively correlated with LIC, moderately correlatied with age, moderately negatively correlated with hepatic and pancreatic T2* values, with r values of 0.833, 0.537, -0.623 and -0.403, respectively (P 0.05). The hepatic and pancreatic T2* values were reduced (P 0.05). Conclusions The patients with β-thalassemia major have prone to suffer from excessive iron deposition in the heart and abdominal organs. The technology of MRI quantification of T2* values could reflect the body iron overload. Key words: Beta-thalassemia; Magnetic resonance imaging; Iron overload

Proteomics analysis of maize (Zea mays L.) grain based on iTRAQ reveals molecular mechanisms of poor grain filling in inferior grains

In maize, inferior grains (IG) located on the upper part of the ear have poor grain filling process compared to superior grains (SG) located on the middle and lower parts of the ear. This difference limits satisfactory yield and quality; however, the underlying molecular mechanisms remain unknown. Here, using the isobaric tag for relative and absolute quantification (iTRAQ) technology, the proteomes of IG and SG during early and middle grain filling stages were investigated. In total, 4720 proteins were identified in maize grain and 305 differentially accumulated proteins (DiAPs) were detected between IG and SG. These DiAPs were involved in diverse cellular and metabolic processes with preferred distribution in protein synthesis/destination and metabolism. Compared to SG, DiAPs related to cell growth/division and starch synthesis were lag-accumulated and down-regulated in IG, respectively, resulting in smaller sink sizes and lower sink activities in IG. Meanwhile, impediment of the glycolysis pathway in IG may lead to reduce energy supply and building materials for substance synthesis. Additionally, reactive oxygen species (ROS) homeostasis and the defense system were disturbed in IG, which might lead to reduce protection against various environmental stresses. The present study provides new information on the proteomic differences between IG and SG, and explains possible molecular mechanisms for poor grain filling in IG.

Preparation and characterization of biodegradable nanocomposites derived from carboxymethyl cellulose and hydroxyapatite

Development of a cost-effective technology for extraction and quantification of carcinogenic and toxic organic materials which are widely used in the industry are critical to humans. Membrane technology received much attention and has already been widely used in this area. In this work, we offer a newly developed bio-based nanocomposite membrane for removal of bisphenol-A (BPA) from water. Three natural components hydroxyapatite (HAp), carboxymethyl cellulose and lysine as a diluent were used for making the bio-based membrane. The membrane was fabricated by two different methods, the conventional casting method and the double decomposition method. Analysis and testing results showed that, membrane produced by the casting method is rough, stiff and partially soluble in water. However, the film made by the double decomposition method is smooth, flexible, and has low water solubility. The physicochemical characteristics of the prepared membranes were determined by Fourier transform infrared spectroscopy (FT-IR) and thermal gravimetric analysis (TGA/DTA). The morphology and components interface were observed by X-ray wide angle (WAXD), scanning electron microscopy (SEM) and electron microscopy (SEM/FEG). The spectral and crystallographic data showed the presence of an effective interaction between hydroxyapatite and CMC plasticized with lysine. Results also show that, the particles size of the composite decrease as the content of CMC increases, with an increase of a 2% by weight of CMC the size increases by 18±3nm. Produced membrane composite could be classified as tri-functional material: it could be useful for extracting toxic material bisphenol A (BPA) from baby food containers; has antimicrobial and antifungal properties; and a valuable candidate for use in bone tissue engineering.

Progress in digital PCR technology and application

Digital PCR is an emerging analysis technology for absolute quantification after realtime-PCR. Through digital PCR, single DNA molecules are distributed into isolated reactions, and the product with fluorescence signal can be detected and analyzed after amplification. With the advantages of higher sensitivity and accuracy, digital PCR, independent of a standard curve, is developing rapidly and applied widely to the next generation sequencing and detection fields, such as gene mutation, copy number variation, microorganism, and genetically modified food. In this article, we reviewed the quantitative method and research progress of digital PCR technology in the main application fields.

Fast resist-activation dosimetry for extreme ultra-violet lithography.

Due to the rather broad band emission spectrum of the extremely hot plasma in its extreme ultra-violet (EUV) source, an EUV lithography scanner also projects out-of-band vacuum- and deep-UV (OoB V/DUV) light on the photoresist on a wafer. As this type of uncontrolled and undesirable light can activate resist chemistry, it will impair the critical dimension uniformity of the patterns, especially across the borders of the fields. Hence, OoB V/DUV quantification technology is required in the pre-production phase. For this reason, the systematic characterization of the EUV-source emission spectrum and the spatial profile of the light as projected on the wafer is indispensable to sustain stable integrated circuit production with EUV lithography. This paper introduces an in-band EUV and OoB V/DUV dosimetry method that is based on enhanced energy sensitivity by resist contrast (EESRC). This dosimetry method is applied in an EUV lithography tool to quantitatively analyze the spatial distribution the resist activation by in-band EUV and OoB V/DUV light, under several exposure conditions. This pragmatic approach can replace the current best-practice of measuring the full spectrum of an EUV light source.

MicroRNA Expression Analysis Using Small RNA Sequencing Discovery and RT-qPCR-Based Validation.

miRNAs are small noncoding RNA molecules that function as regulators of gene expression. Deregulated miRNA expression has been reported in various diseases including cancer. Due to their small size and high degree of homology, accurate quantification of miRNA expression is technically challenging. In this chapter, we present two different technologies for miRNA quantification: small RNA sequencing and RT-qPCR.

ITRAQ-Based Proteomics Analysis of Acute Lung Injury Induced by Oleic Acid in Mice

Background/Aims: This study was conducted to investigate the relationship between differentially expressed proteins (DEPs) and the pathogenesis of oleic acid (OA)-induced acute lung injury (ALI) in mice. Methods: Eight-week-old male C57BL/6 mice were injected with OA through the tail vein and sacrificed 6 hours after OA administration to identify protein expression levels in lung tissue using isobaric tags for relative and absolute quantification (iTRAQ) technology. Then, DEPs such as antithrombin III (AT III), 12-lipoxygenase (12-LO), dedicator of cytokinesis 2 (DOCK2), polycystin-2 and plasminogen were identified by western blotting. Subsequently, we focused on investigating the effect of AT III on endothelial integrity using siRNA interference technology. The levels of IL-6, IL-1β, TNF-α and TGF-β expression were detected using an enzyme-linked immunosorbent assay (ELISA). Alterations in the tight junction component ZO-1 and the phosphorylation of myosin light chain (pMLC) were determined by western blotting. The stress fiber F-actin were also detected by immunofluorescence staining. In addition, endothelial permeability was determined via a transwell permeability assay. Results: A total of 5152 proteins were found to be expressed in lung tissues from the OA-treated and saline-treated mice. Among these proteins, 849 were differentially expressed between the two groups, including 545 upregulated and 304 downregulated proteins. After AT III knockdown, the levels of inflammatory factors and endothelial permeability were elevated, the expression of ZO-1 was decreased, and the expression of F-actin and pMLC was increased. All these results illustrated that AT III knockdown exaggerated the disruption of endothelial integrity mediated by OA. Conclusion: These findings using iTRAQ technology demonstrate, for the first time, differences in the lung tissue expression levels of proteins between OA-treated mice and saline-treated mice. This study reveals that 12-LO, DOCK2 and especially AT III may be candidate biomarkers for OA-induced acute lung injury.

Three-dimensional automated reporter quantification (3D-ARQ) technology enables quantitative screening in retinal organoids.

The advent of stem cell-derived retinal organoids has brought forth unprecedented opportunities for developmental and physiological studies, while presenting new therapeutic promise for retinal degenerative diseases. From a translational perspective, organoid systems provide exciting new prospects for drug discovery, offering the possibility to perform compound screening in a three-dimensional (3D) human tissue context that resembles the native histoarchitecture and to some extent recapitulates cellular interactions. However, inherent variability issues and a general lack of robust quantitative technologies for analyzing organoids on a large scale pose severe limitations for their use in translational applications. To address this need, we have developed a screening platform that enables accurate quantification of fluorescent reporters in complex human iPSC-derived retinal organoids. This platform incorporates a fluorescence microplate reader that allows xyz-dimensional detection and fine-tuned wavelength selection. We have established optimal parameters for fluorescent reporter signal detection, devised methods to compensate for organoid size variability, evaluated performance and sensitivity parameters, and validated this technology for functional applications.

Validation of a Multimodality Flow Phantom and Its Application for Assessment of Dynamic SPECT and PET Technologies.

Simple and robust techniques are lacking to assess performance of flow quantification using dynamic imaging. We therefore developed a method to qualify flow quantification technologies using a physical compartment exchange phantom and image analysis tool. We validate and demonstrate utility of this method using dynamic PET and SPECT. Dynamic image sequences were acquired on two PET/CT and a cardiac dedicated SPECT (with and without attenuation and scatter corrections) systems. A two-compartment exchange model was fit to image derived time-activity curves to quantify flow rates. Flowmeter measured flow rates (20-300 mL/min) were set prior to imaging and were used as reference truth to which image derived flow rates were compared. Both PET cameras had excellent agreement with truth ( [Formula: see text]). High-end PET had no significant bias (p > 0.05) while lower-end PET had minimal slope bias (wash-in and wash-out slopes were 1.02 and 1.01) but no significant reduction in precision relative to high-end PET (<15% vs. <14% limits of agreement, p > 0.3). SPECT (without scatter and attenuation corrections) slope biases were noted (0.85 and 1.32) and attributed to camera saturation in early time frames. Analysis of wash-out rates from non-saturated, late time frames resulted in excellent agreement with truth ( [Formula: see text], slope = 0.97). Attenuation and scatter corrections did not significantly impact SPECT performance. The proposed phantom, software and quality assurance paradigm can be used to qualify imaging instrumentation and protocols for quantification of kinetic rate parameters using dynamic imaging.

DeeperBind: Enhancing Prediction of Sequence Specificities of DNA Binding Proteins.

Transcription factors (TFs) are macromolecules that bind to cis-regulatory specific sub-regions of DNA promoters and initiate transcription. Finding the exact location of these binding sites (aka motifs) is important in a variety of domains such as drug design and development. To address this need, several in vivo and in vitro techniques have been developed so far that try to characterize and predict the binding specificity of a protein to different DNA loci. The major problem with these techniques is that they are not accurate enough in prediction of the binding affinity and characterization of the corresponding motifs. As a result, downstream analysis is required to uncover the locations where proteins of interest bind. Here, we propose DeeperBind, a long short term recurrent convolutional network for prediction of protein binding specificities with respect to DNA probes. DeeperBind can model the positional dynamics of probe sequences and hence reckons with the contributions made by individual sub-regions in DNA sequences, in an effective way. Moreover, it can be trained and tested on datasets containing varying-length sequences. We apply our pipeline to the datasets derived from protein binding microarrays (PBMs), an in-vitro high-throughput technology for quantification of protein-DNA binding preferences, and present promising results. To the best of our knowledge, this is the most accurate pipeline that can predict binding specificities of DNA sequences from the data produced by high-throughput technologies through utilization of the power of deep learning for feature generation and positional dynamics modeling.

Serum neurofilament light protein predicts clinical outcome in traumatic brain injury.

Axonal white matter injury is believed to be a major determinant of adverse outcomes following traumatic brain injury (TBI). We hypothesized that measurement of neurofilament light protein (NF-L), a protein found in long white-matter axons, in blood samples, may serve as a suitable biomarker for neuronal damage in TBI patients. To test our hypotheses, we designed a study in two parts: i) we developed an immunoassay based on Single molecule array technology for quantification of NF-L in blood, and ii) in a proof-of-concept study, we tested our newly developed method on serial serum samples from severe TBI (sTBI) patients (n = 72) and controls (n = 35). We also compared the diagnostic and prognostic utility of NF-L with the established blood biomarker S100B. NF-L levels were markedly increased in sTBI patients compared with controls. NF-L at admission yielded an AUC of 0.99 to detect TBI versus controls (AUC 0.96 for S100B), and increased to 1.00 at day 12 (0.65 for S100B). Importantly, initial NF-L levels predicted poor 12-month clinical outcome. In contrast, S100B was not related to outcome. Taken together, our data suggests that measurement of serum NF-L may be useful to assess the severity of neuronal injury following sTBI.

Proteomic analysis of maize grain development using iTRAQ reveals temporal programs of diverse metabolic processes.

BackgroundGrain development in maize is an essential process in the plant’s life cycle and is vital for use of the plant as a crop for animals and humans. However, little is known regarding the protein regulatory networks that control grain development. Here, isobaric tag for relative and absolute quantification (iTRAQ) technology was used to analyze temporal changes in protein expression during maize grain development.ResultsMaize grain proteins and changes in protein expression at eight developmental stages from 3 to 50 d after pollination (DAP) were performed using iTRAQ-based proteomics. Overall, 4751 proteins were identified; 2639 of these were quantified and 1235 showed at least 1.5-fold changes in expression levels at different developmental stages and were identified as differentially expressed proteins (DEPs). The DEPs were involved in different cellular and metabolic processes with a preferential distribution to protein synthesis/destination and metabolism categories. A K-means clustering analysis revealed coordinated protein expression associated with different functional categories/subcategories at different development stages.ConclusionsOur results revealed developing maize grain display different proteomic characteristics at distinct stages, such as numerous DEPs for cell growth/division were highly expressed during early stages, whereas those for starch biosynthesis and defense/stress accumulated in middle and late stages, respectively. We also observed coordinated expression of multiple proteins of the antioxidant system, which are essential for the maintenance of reactive oxygen species (ROS) homeostasis during grain development. Particularly, some DEPs, such as zinc metallothionein class II, pyruvate orthophosphate dikinase (PPDK) and 14-3-3 proteins, undergo major changes in expression at specific developmental stages, suggesting their roles in maize grain development. These results provide a valuable resource for analyzing protein function on a global scale and also provide new insights into the potential protein regulatory networks that control grain yield and quality.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-016-0878-1) contains supplementary material, which is available to authorized users.