Characterization of two O-methyltransferases involved in the biosynthesis of O-methylated catechins in tea plant.

Tea is known for having a high catechin content, with the main component being (-)-epigallocatechin gallate (EGCG), which has significant bioactivities, including potential anti-cancer and anti-inflammatory activity. The poor intestinal stability and permeability of EGCG, however, undermine these health-improving benefits. O-methylated EGCG derivatives, found in a few tea cultivars in low levels, have attracted considerable interest due to their increased bioavailability. Here, we identify two O-methyltransferases from tea plant: CsFAOMT1 that has a specific O-methyltransferase activity on the 3''-position of EGCG to generate EGCG3''Me, and CsFAOMT2 that predominantly catalyzes the formation of EGCG4″Me. In different tea tissues and germplasms, the transcript levels of CsFAOMT1 and CsFAOMT2 are strongly correlated with the amounts of EGCG3''Me and EGCG4''Me, respectively. Furthermore, the crystal structures of CsFAOMT1 and CsFAOMT2 reveal the key residues necessary for 3''- and 4''-O-methylation. These findings may provide guidance for the future development of tea cultivars with high O-methylated catechin content.

Oxidant-Induced Bioconjugation for Protein Labeling in Live Cells.

Chemical proteomics is a powerful technology that can be used in the studies of the functions of uncharacterized proteins in the human proteome. It relies on a suitable bioconjugation strategy for protein labeling. This could be either a UV-responsive photo-crosslinker or an electrophilic warhead embedded in chemical probes that can form covalent bonds with target proteins. Here, we report a new protein-labeling strategy in which a nitrile oxide, a highly reactive intermediate that reacts with proteins, can be efficiently generated by the treatment of oximes with a water-soluble and a minimally toxic oxidant, phenyliodine bis (trifluoroacetate) (PIFA). The resulting intermediate can rapidly bioconjugate with amino acid residues of target proteins, thus enabling target identification of oxime-containing bioactive molecules. Excellent chemoselectivity of cysteine residues by the nitrile oxide was observed, and over 4000 reactive and/or accessible cysteines, including KRAS G12C, have been successfully characterized by quantitative chemical proteomics. Some of these residues could not be detected by conventional cysteine reagents, thus demonstrating the complementary utility of this method.

Preparation and Characterization of Polysaccharides from Turpiniae Folium and Its Antioxidative, Anti-Inflammatory Activities and Antiproliferative Effect on VSMCs.

Turpiniae Folium, the dried leaves of Turpinia arguta Seem., is a kind of historic traditional Chinese medicine. Here, based on our previous study, we extracted the Turpiniae Folium polysaccharides (TFP) and isolated three polysaccharide fractions from TFP. Then, TFP and one of the major polysaccharide fractions (TFP-1a) were identified through HPLC, HPGPC, and ATR-FTIR. Furthermore, the evaluations of their antioxidative, anti-inflammatory activities and inhibitory effect on angiotensin II-induced vascular smooth muscle cells (VSCMs) proliferation in vitro were conducted. Both TFP and TFP-1a showed strong hydroxyl radical scavenging, DPPH radical scavenging, and Fe2+ chelating activities, and exerted strong anti-inflammatory activity. Moreover, TFP and TFP-1a also possessed a strong inhibitory effect on Ang II-induced VSCMs proliferation. On these premises, we inferred that TFP and TFP-1a could be potential and promising natural antioxidants, anti-inflammatory agents, and implicated to treat cardiovascular disease.

Investigation of the idiosyncratic hepatotoxicity of Polygonum multiflorum Thunb. through metabolomics using GC-MS.

BACKGROUND: The idiosyncratic hepatotoxicity of Polygonum multiflorum (PM) has attracted considerable interest, but the idiosyncratically hepatotoxic components and endogenous metabolite changes resulting from idiosyncratic hepatotoxicity of PM are not well understood. The aim of this study was to identify the idiosyncratically hepatotoxic components and potential endogenous metabolic biomarkers for PM-induced liver injury. METHODS: Serum biochemical indicators and hematoxylin and eosin (H&E) staining were evaluated to identify pathological changes. Gas chromatography/mass spectrometry (GC-MS) was performed to identify changes in metabolic biomarkers. Orthogonal projection to latent structures discriminant analysis (OPLS-DA) was applied to determine group clustering trends and differential metabolites. RESULTS: The results for the liver index, the liver function index and liver pathology showed that Polygonum multiflorum ethanol extract (PME), 50% ethanol elution fractions and tetrahydroxystilbene glucoside (TSG) from PME can induce idiosyncratic hepatotoxicity. TSG was the main idiosyncratically hepatotoxic component. Forty endogenous metabolites were identified in the rat liver. Six biomarkers, including lower levels of L-valine and higher levels of 3-hydroxybutyric acid, hexadecanoic acid, ribose, phosphoric acid and oxalic acid, were related to PM-induced liver injury. These differential biomarkers led to disruptions in amino acid, fatty acid, oxalate, energy and glucose metabolism. A total of 32 types of endogenous metabolites were identified in rat serum. Ten biomarkers were related to the liver injury induced by TSG, including lower levels of L-valine and L-proline and higher levels of urea, caproic acid, DL-malic acid, D-mannose, 3-hydroxybutyric acid, D-galactose, octadecane and hexadecanoic acid. These differential biomarkers led to disruptions in amino acid, glucose and fat metabolism. The mechanism of idiosyncratic hepatotoxicity in PM involves TSG-induced disruptions in amino acid metabolism, lipid metabolism, energy metabolism and glucose metabolism. CONCLUSIONS: These findings reflect the material basis and metabolic mechanism of idiosyncratic PM hepatotoxicity.

Combination and distribution characteristics of syndromes related to traditional Chinese medicine in patients with chronic heart failure: Protocol for a clinical study.

INTRODUCTION: Chronic heart failure has become one of the main diseases endangering human health in the 21st century. It is characterized by high morbidity and high mortality. With the continuous in-depth study of Traditional Chinese medicine, the treatment of heart failure by Tradional Chinese medicine has made significant progress, especially in improving the clinical symptoms of patients, controlling the development of the disease, and improving the quality of life of patients. METHODS/DESIGN: This will be a retrospective, single-blind clinical observational study. All participants will receive chronic heart failure routine treatment and care. The researcher will fill in the case information collection form and collect multiple clinical diagnosis and treatment information. DISCUSSION: At present, there is very little research on the elements of chronic heart failure syndrome, and more exploration and excavation in this area are needed. So we designed this program. We aim to explore the distribution characteristics of Traditional Chinese medicine syndrome elements and combinations of chronic heart failure patients, and analyze the relationship between syndrome elements and related influencing factors. TRIAL REGISTRATION: ClinicalTrials.gov,ChiCTR2000034555, Registered on 18 May 2020.

Distribution of traditional Chinese medicine syndromes in type 2 diabetes mellitus with chronic heart failure: A clinical study.

INTRODUCTION: The incidence of type 2 diabetes has been increasing year by year in recent years. Type 2 diabetes is an important risk factor in the occurrence and development of heart failure, and it is the second potential risk factor after coronary artery disease. At present, there is no unified etiology, pathogenesis, and syndrome differentiation criteria for type 2 diabetes with chronic heart failure, and it is susceptible to subjective factors. Therefore, standardized, objective, and standardized research is needed to provide reference and guidance for clinical diagnosis and treatment. In this study, the theory of syndrome differentiation is used to initially explore the distribution of traditional Chinese medicine syndromes in patients with type 2 diabetes and chronic heart failure through case data collection, syndrome extraction, and clinical data analysis. METHODS/DESIGN: In this study, we will collect at least 500 cases of type 2 diabetes with chronic heart failure that meet the standard outpatient and hospitalization, and fill out the case information collection form. Then we will collect a number of clinical diagnosis and treatment information, and judge the syndrome based on the sum of the contribution of each syndrome to the relevant syndrome. We will use Microsoft Excel to establish a database, enter the relevant diagnosis and treatment, and syndrome information of the case information collection table, and verify and correct in time to ensure the accuracy of the data. DISCUSSION: This study will provide reference and guidance for the clinical diagnosis and treatment of type 2 diabetes with chronic heart failure. TRIAL REGISTRATION: ClinicalTrials.gov, ChiCTR2000033010, Registered on May 18, 2020.

Characterization and anti-uterine tumor effect of extract from Prunella vulgaris L.

BACKGROUND: The flowers and dried fruit spikes of Prunella vulgaris L. (P. vulgaris L.) have been widely used in traditional Chinese medicine and food. P. vulgaris L. is regarded as a good option for treating uterine myoma (UM). However, scientific evidence of anti-UM activity of the extract of P. vulgaris L. (PVE) is lacking. The present study aimed to characterize the chemical composition of PVE and evaluate the pharmacodynamics and mechanism of PVE against UM. METHODS: The chemical composition of PVE was analyzed by GC-MS. MTT was used to screen and evaluate cell proliferation and toxicity. Double fluorescence flow cytometry method were used to determine the apoptosis and cell cycle progression of UM cells under PVE treatment. The anti-UM activity of PVE was investigated by using a specific-pathogen-free (SPF) rat model of UM. TUNEL staining was used to detect the apoptosis of UM cells. The concentrations of estrogen and progesterone in the serum of SPF rats were detected by ELISA. The expression levels of PCNA, estrogen receptor alpha, estrogen receptor beta, progesterone receptor, survivin, caspase-3, Bax and Bcl-2 in the uterus of SPF rats was detected by immunohistochemistry (IHC). RESULTS: The extraction rate of PVE was 8.1%. The main components were squalene (28.3%), linoleic acid (9.96%), linolenic acid (9.95%), stearic acid (6.26%) and oleic acid (5.51%). In vitro, PVE had significant anti-human UM cell activity, exhibited no drug toxicity, promoted the apoptosis of human UM cells, and inhibited the transition of UM cells from the G0/G1 stage into the G2 stage, in which DNA replication occurs. In vivo, PVE had significant anti-UM activity. PVE decreased the concentrations of estrogen and progesterone and downregulated the expression levels of the estrogen and progesterone receptors through the estrogen signaling pathway. PVE also promoted the apoptosis of UM cells by downregulating the expression levels of the survivin and Bcl-2 proteins and upregulating the expression levels of caspase-3 and Bax through the mitochondria-mediated apoptotic pathway. CONCLUSION: PVE has marked anti-UM activity. PVE can be used as an ideal candidate drug to treat UM.

Yangxinkang tablet protects against cardiac dysfunction and remodelling after myocardial infarction in rats through inhibition of AMPK/mTOR-mediated autophagy.

Context: Acute myocardial infarction (AMI) is defined as myocardial necrosis. Clinicians use the traditional Chinese patent medicine Yangxinkang Tablet (YXK) to treat chronic heart failure.Objective: To explore the effects of YXK on heart injury following AMI and the underlying mechanisms.Materials and methods: The AMI model was produced in Wistar rats by permanent ligation of the left anterior descending coronary artery. Rats were divided into the following five groups: Sham (n = 6), MI (Model, n = 10), AICAR (AMPK agonist, 50 mg/kg/d, i.p., n = 10), Compound C (AMPK inhibitor, 10 mg/kg/d, i.p., n = 10), and YXK (0.72 g/kg/d, gavage, n = 10) groups. Cardiac function, cardiac fibrosis, apoptosis, and expression of p-AMPK, p-mTOR, and autophagy-related proteins was measured after 4 weeks of treatment after the successful modelling of the AMI.Results: Compared to MI group, both YXK and AMPK inhibitor improved cardiac dysfunction and reduced cardiac fibrosis (15.6 ± 2.3; 22.6 ± 4.6 vs. 34.6 ± 4.3%) and myocardial cell apoptosis (12 ± 3.67; 25.6 ± 6.8 vs. 54 ± 4.8%). Futhermore, YXK and AMPK inhibitor significantly decreased p-AMPK expression by 11.05% and 14.64%, LC3II/I by 25.08% and 35.28% and Beclin-1 by 66.71% and 33.85%, increased p-mTOR by 22.14% and 47.46% and p62 by 70.83% and 18.58%.Conclusions: The underlying mechanism appears to include suppression of autophagy via inhibiting AMPK/mTOR signalling, suggesting that YXK may serve as a potentially effective Chinese herbal compound for suppressing cardiac fibrosis in heart injury.

Identification and characterization of N9-methyltransferase involved in converting caffeine into non-stimulatory theacrine in tea.

Caffeine is a major component of xanthine alkaloids and commonly consumed in many popular beverages. Due to its occasional side effects, reduction of caffeine in a natural way is of great importance and economic significance. Recent studies reveal that caffeine can be converted into non-stimulatory theacrine in the rare tea plant Camellia assamica var. kucha (Kucha), which involves oxidation at the C8 and methylation at the N9 positions of caffeine. However, the underlying molecular mechanism remains unclear. Here, we identify the theacrine synthase CkTcS from Kucha, which possesses novel N9-methyltransferase activity using 1,3,7-trimethyluric acid but not caffeine as a substrate, confirming that C8 oxidation takes place prior to N9-methylation. The crystal structure of the CkTcS complex reveals the key residues that are required for the N9-methylation, providing insights into how caffeine N-methyltransferases in tea plants have evolved to catalyze regioselective N-methylation through fine tuning of their active sites. These results may guide the future development of decaffeinated drinks.

Extraction, Characterization, Antioxidant, and Immunostimulatory Activities of Polysaccharides from Hedyotis corymbosa.

In this study, optimization of enzyme-assisted extraction, purification, characterization, and its bioactivities of polysaccharides from Hedyotis corymbosa (HCP) was investigated. It was found that the optimum extraction conditions were 3% of enzyme concentration (X 1 ), 30 of liquid-to-solid ratio (X 2 ), 56°C of extraction temperature (X 3 ), 200W of ultrasonic power (X 4 ), 10 min of extraction time (X 5 ), and 5 of pH value (X 6 ). Under optimum conditions, the experimental yield (4.10 ± 0.16%) was closed to the predicted value (4.02%). The crude HCP was further purified using DEAE-52 and Sephadex G-150 gel column, and a major polysaccharide fraction from HCP, designed as HCP-1a with molecular weight of 33.9 kDa, was obtained. The HCP and HCP-1a were characterized by chemical analysis, FT-IR, and HPLC. For antioxidant activities in vitro, HCP possessed strong hydroxyl radical scavenging, DPPH radical scavenging, and Fe2+ chelating activities. In subsequent immunostimulatory studies, significantly decreased NO, IL-1ß, and TNF-α concentrations were observed in both of HCP and HCP-1a treated RAW264.7 cells. Therefore, this study may indicate some insights into the application of polysaccharides from Hedyotis corymbosa as potential natural antioxidants and immunostimulants.

[Extraction of flavonoids in Prunella vulgaris based on deep eutectic solvent method：application of new green solvent].

Flavonoids have attracted much attention due to their good anti-inflammatory, anti-oxidation and anti-tumor effects. At present, the extraction of flavonoids is mainly based on organic solvent, while the researches on the use of green and safe solvents are quite limited. Therefore, in the present study, different types of deep eutectic solvents (DESs) were applied to investigate their effect on extraction of flavonoids and optimize the process, also investigate the recovery efficiency of DESs and evaluate the recovery method for total flavonoids. The extraction yield of the total flavonoids acted as the comprehensive evaluation indexes, and a central composite design (CCD) of response surface methodology (RSM) was employed to further optimize the alcohol-based DES extraction conditions. The results showed that the optimized extraction conditions were as follows: water-DES ratio of 27%, solid-liquid ratio of 15 mL·g⁻¹, extraction temperature of 83 °C and extraction time of 42 min in ChCl-glycerol at 1:4 ratio. Under these conditions, the mean experimental value of the extraction yield (75.05 mg·g⁻¹) corresponded well with the predicted value (77.86 mg·g⁻¹). Moreover, these experimental results showed more advantages such as in higher efficiency, economy and environmental protection as compared with previously reported conventional extraction methods. In addition，the recovery yield of the total flavonoids from the DESs extraction solution achieved 97.88% by using AB-8 macroporous resin, and 88.12% desorption ratio can be achieved by 100% ethanol with 5 times resin content. After the above treated DESs were collected, the extraction yield with the same method reached 95.23%, indicating that the method of macroporous resin can be used for efficient and simple recovery and reuse. This study suggests that DESs can be used as a kind of sustainable and efficient natural extraction solvents for extraction of flavonoids from Prunella vulgaris.

A modified multiscale peak alignment method combined with trilinear decomposition to study the volatile/heat-labile components in Ligusticum chuanxiong Hort - Cyperus rotundus rhizomes by HS-SPME-GC/MS.

Head Space/Solid Phase Micro-Extraction (HS-SPME) coupled with Gas Chromatography/Mass Spectrometer (GC/MS) was used to determine the volatile/heat-labile components in Ligusticum chuanxiong Hort - Cyperus rotundus rhizomes. Facing co-eluting peaks in k samples, a trilinear structure was reconstructed to obtain the second-order advantage. The retention time (RT) shift with multi-channel detection signals for different samples has been vital in maintaining the trilinear structure, thus a modified multiscale peak alignment (mMSPA) method was proposed in this paper. The peak position and peak width of representative ion profile were firstly detected by mMSPA using Continuous Wavelet Transform with Haar wavelet as the mother wavelet (Haar CWT). Then, the raw shift was confirmed by Fast Fourier Transform (FFT) cross correlation calculation. To obtain the optimal shift, Haar CWT was again used to detect the subtle deviations and be amalgamated in calculation. Here, to ensure there is no peaks shape alternation, the alignment was performed in local domains of data matrices, and all data points in the peak zone were moved via linear interpolation in non-peak parts. Finally, chemical components of interest in Ligusticum chuanxiong Hort - Cyperus rotundus rhizomes were analyzed by HS-SPME-GCMS and mMSPA-alternating trilinear decomposition (ATLD) resolution. As a result, the concentration variation between herbs and their pharmaceutical products can provide a scientific basic for the quality standard establishment of traditional Chinese medicines.

[Analysis on multiple pharmaceutical ingredients and antioxidant capacities of Prunellae Spica based on multivariate statistical analysis].

Prunellae Spica is a perennial edible and medicinal plant, rich in antioxidant substances. Total flavonoids (TFC), Phenolics (TPC), triterpenoids (TSC), polysaccharides (PC) and their antioxidant capacities (by the FRAP, DPPH and ABTS⁺ methods) of ethyl acetate fraction, n-butanol fraction and other fractions of aqueous extract from Prunellae Spica were investigated in this study. Then the multivariate statistical method was adopted to analyze the relationship between the multiple pharmaceutical ingredients and antioxidant capacities of Prunellae Spica. The results showed that ethyl acetate fraction had relatively high concentration of TFC (0.61±0.10) g·g⁻¹DW, TPC (0.52±0.09) g·g⁻¹DW, and TSC (0.21±0.03) g·g⁻¹DW, with high scavenging capacity of DPPH (3.1±0.38) mmol·L⁻¹·g⁻¹DW and FRAP (2.56±0.35) mmol·L⁻¹·g⁻¹DW. Hierarchical clustering analysis (HCA) and principal component analysis (PCA) results indicated the information from chemical compositions and antioxidant capacity can represent the "differences" of different fractions. Canonical correlation analysis (CCorA) revealed a high positive correlation between the amounts of multiple chemical compositions and the antioxidant capacities (r=0.970 0), and the first canonical variate had been reached. Moreover, ABTS⁺ method showed a low response to the compositions of different fractions, so this method may not be suitable for evaluation of Prunellae Spica antioxidant capacities, while DPPH evaluation method was more suitable for TSC and TPC. The results of this study have important reference significance for the evaluation method on antioxidant activity of Prunellae Spica in the field of food or medicine as well as for the development of related extracts.

Robust alignment of chromatograms by statistically analyzing the shifts matrix generated by moving window fast Fourier transform cross-correlation.

Retention time shift is one of the most challenging problems during the preprocessing of massive chromatographic datasets. Here, an improved version of the moving window fast Fourier transform cross-correlation algorithm is presented to perform nonlinear and robust alignment of chromatograms by analyzing the shifts matrix generated by moving window procedure. The shifts matrix in retention time can be estimated by fast Fourier transform cross-correlation with a moving window procedure. The refined shift of each scan point can be obtained by calculating the mode of corresponding column of the shifts matrix. This version is simple, but more effective and robust than the previously published moving window fast Fourier transform cross-correlation method. It can handle nonlinear retention time shift robustly if proper window size has been selected. The window size is the only one parameter needed to adjust and optimize. The properties of the proposed method are investigated by comparison with the previous moving window fast Fourier transform cross-correlation and recursive alignment by fast Fourier transform using chromatographic datasets. The pattern recognition results of a gas chromatography mass spectrometry dataset of metabolic syndrome can be improved significantly after preprocessing by this method. Furthermore, the proposed method is available as an open source package at https://github.com/zmzhang/MWFFT2.

Andrographolide induced acute kidney injury: analysis of 26 cases reported in Chinese Literature.

AIM: Some Chinese herbs have been known for their kidney toxicity. Andrographolide, the primary component of a traditional medicinal herb, Andrographis paniculata, is widely used in China for the treatment of upper and lower respiratory tract infection, and dysentery etc. The aim of the study was to identify and summarize any case of kidney injury attributed to its use in the Chinese literature. METHODS: A systemic analysis of the Chinese literature from January 1978 to August 2013 was conducted of case reports of andrographolide induced acute kidney injury (AKI). RESULTS: We identified 26 cases of andrographolide induced AKI (22 males and four females), with an average age of 31.3 years (range: 21 months to 47 years). 100-750 mg (58% 500 mg) of andrographolide was administered in 100-500 mL 5% glucose solution or normal saline by intravenous drip once a day. The adverse event appeared after one to six doses (19 [73.1%] patients got only one dose; cumulative dose 690 ± 670 mg) of andrographolide was given, or 0-96 h (median 1 h) after andrographolide was given. The symptoms included flank pain in 23 cases (88.5%), decreased urine volume in five cases (19.2%), and nausea or vomiting in six cases (23.1%). Laboratory tests showed maximum creatinine 352.8 ± 184.1 (158-889) µmol/L and blood urea nitrogen 12.1 ± 7.6 (4.0-40.6) mmol/L. Urine analysis showed proteinuria in 10 (38.5%) cases and occult blood in eight (30.8%) cases. Kidney biopsy was carried out in two cases and both revealed acute tubular necrosis. Management of this adverse event included withdrawal of the culprit drug, conservative therapy, and renal replacement therapy (six cases, 23.1%). All the patients recovered and were discharged with a normal or close to normal serum creatinine. Their average length of hospital stay was 12.1 ± 4.8 days. CONCLUSIONS: Acute kidney injury may occur shortly after intravenous infusion of andrographolide, with symptoms including flank pain, decreased urine output, and nausea or vomiting. The pathological change might be acute tubular necrosis. Renal replacement therapy may be needed in some patients and with a good recovery rate. The mechanisms of andrographolide induced AKI need to be further studied.

Application of random forests to select premium quality vegetable oils by their fatty acid composition.

In order to discriminate premium quality from inexpensive edible oils, the fatty acid profiles of tea, rapeseed, corn, sunflower and sesame oil were compared with the ones from extra virgin olive oil (EVOO). Fatty acid methyl esters were quantified by GC/MS. Principal component analysis (PCA) and random forests (RF) were applied to cluster the samples. RF showed a better ability of discrimination and also revealed the contribution of each variable to the clustering model. The multidimensional scaling (MDS) plot of the RF proximity matrix demonstrated that tea oil was similar to EVOO. Meanwhile, it was observed that the total content of cis-monounsaturated fatty acids (79.48%) in tea oil was close to EVOO (80.71%), especially the oleic acid (77.38% and 77.45%, respectively). The results suggest that tea oil might be a good edible oil choice, considering the high oleic acid content and similar fatty acid profiles compared to those of EVOO.

Nonlinear alignment of chromatograms by means of moving window fast Fourier transfrom cross-correlation.

The preprocessing of chromatograms is essential to modern chromatography for further qualitative and quantitative analysis, especially when chromatographic instruments are used for herb products analysis involving large number of samples. To accurately compare and analyze the obtained chromatograms, it is necessary to preprocess, especially align retention time shifts. Here moving window fast Fourier transform (FFT) cross-correlation is introduced to perform nonlinear alignment of high-throughput chromatograms. Since elution characteristics of chromatograms will produce local similarity in retention time shifts, moving window procedure seems to be a better substitute of segmentation steps. The retention time shifts can be calculated and accelerated by FFT cross-correlation. The artifacts can be detected and eliminated from the retention time shifts profile since the continuity of moving window procedure. The proposed method is demonstrated in comparison with recursive alignment by FFT on chromatographic datasets from herb products analysis. It is shown that the proposed method can address nonlinear retention time shift problem in chromatograms with the simple moving window procedure, which will not introduce segments size optimization problem. In additional, the parameters are intuitive and easy to adjust, which makes it off-the-shelf toolbox for alignment of chromatograms.

Multiscale peak alignment for chromatographic datasets.

Chromatography has been extensively applied in many fields, such as metabolomics and quality control of herbal medicines. Preprocessing, especially peak alignment, is a time-consuming task prior to the extraction of useful information from the datasets by chemometrics and statistics. To accurately and rapidly align shift peaks among one-dimensional chromatograms, multiscale peak alignment (MSPA) is presented in this research. Peaks of each chromatogram were detected based on continuous wavelet transform (CWT) and aligned against a reference chromatogram from large to small scale gradually, and the aligning procedure is accelerated by fast Fourier transform cross correlation. The presented method was compared with two widely used alignment methods on chromatographic dataset, which demonstrates that MSPA can preserve the shapes of peaks and has an excellent speed during alignment. Furthermore, MSPA method is robust and not sensitive to noise and baseline. MSPA was implemented and is available at http://code.google.com/p/mspa.