BioSunMS: a plug-in-based software for the management of patients information and the analysis of peptide profiles from mass spectrometry

Background  

With wide applications of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF MS), statistical comparison of serum peptide profiles and management of patients information play an important role in clinical studies, such as early diagnosis, personalized medicine and biomarker discovery. However, current available software tools mainly focused on data analysis rather than providing a flexible platform for both the management of patients information and mass spectrometry (MS) data analysis.     

Rapid differentiation of Mycobacterium xenopi from mycobacteria of the Mycobacterium avium-intracellulare complex by pyrolysis mass spectrometry.

Thirty four cultures of slow growing, Tween-80 negative mycobacteria were analysed by pyrolysis mass spectrometry. The results showed that pyrolysis mass spectrometry could positively distinguish strains of Mycobacterium xenopi from those of the Mycobacterium avium-intracellulare (MAI) complex. Pyrolysis mass spectrometry may be a useful technique for the rapid characterisation of non-tuberculous mycobacteria in such clinical settings as their isolation from immunocompromised patients-for example, those with AIDS.     

基质辅助激光解析离子-飞行时间质谱仪在临床分离革兰阴性杆菌鉴定中的应用

目的 了解基质辅助激光解析离子-飞行时间质谱仪(MALDI-TOF-MS)在临床分离革兰阴性杆菌鉴定中的应用,为临床医师正确诊断提供科学依据.方法 采用 MALDI-TOF-MS技术对1625株临床常见革兰阴性杆菌进行鉴定.VITEK MS鉴定结果与VITEK-2 Compact全自动微生物鉴定系统对比,结果差异的菌株采用16S rDNA测序验证.结果 VITEK MS共鉴定出常见革兰阴性杆菌1625株,肠杆菌科1219株共6种,非发酵菌属406株共4种.VITEK MS系统与VITEK-2 Compact系统鉴定结果比较,120株常见革兰阴性杆菌鉴定符合率为95.83%.5株鉴定结果不符菌株用16S rDNA测序验证,与VITEK-2 Compact 鉴定符合率为2/5(40%),与VITEK MS鉴定符合率为3/5(60%).结论 VITEK MS能快速鉴定出常见革兰阴性杆菌,为临床治疗及鉴别感染病原菌提供了快速的筛选方法.     

Detection of RET proto-oncogene codon 634 mutations using mass spectrometry

 Mutations located in the RET proto-oncogene at codon 634 associated with multiple endocrine neoplasia type 2A and medullary thyroid carcinoma are detected by low-resolution and high-resolution mass spectrometry schemes not requiring labeling or electrophoretic separation of diagnostic products. The former requires measurement by matrix-assisted laser desorption ionization time-of-flight mass spectrometry of 21- to 27-mer oligonucleotides generated by a primer oligo base extension reaction. The latter is based upon direct measurement of artificial products which include the mutation site using matrix-assisted laser desorption ionization Fourier transform mass spectrometry. In this feasibility study a synthetic 25-mer representing the wildtype allele (7660.3 Da) was easily distinguished from G to A (7644.3 Da) and G to T (7635.3 Da) mutant alleles; the mutant alleles, which differed in mass by only 9.0 Da, were easily resolved when analyzed as a mixture. The results of both detection schemes were highly accurate and reliable, indicating mass spectrometry to be a high-quality alternative for future DNA diagnostics performed in clinical laboratories and genetic profiling studies. Received: 24 February 1997 / Accepted: 2 June 1997     

A machine learning perspective on the development of clinical decision support systems utilizing mass spectra of blood samples

Currently, the best way to reduce the mortality of cancer is to detect and treat it in the earliest stages. Technological advances in genomics and proteomics have opened a new realm of methods for early detection that show potential to overcome the drawbacks of current strategies. In particular, pattern analysis of mass spectra of blood samples has attracted attention as an approach to early detection of cancer. Mass spectrometry provides rapid and precise measurements of the sizes and relative abundances of the proteins present in a complex biological/chemical mixture. This article presents a review of the development of clinical decision support systems using mass spectrometry from a machine learning perspective. The literature is reviewed in an explicit machine learning framework, the components of which are preprocessing, feature extraction, feature selection, classifier training, and evaluation.     

Monitoring of hepatitis C virus quasispecies in chronic infection by matrix-assisted laser desorption ionization-time of flight mass spectrometry mutation detection

Using both a mass spectrometry-based method and the classical method of cloning and sequencing, we demonstrated weekly changes in the hypervariable region 1 quasispecies of a chimpanzee infected with an infectious clone, coinciding with neutralizing antibody emergence. We also used the mass spectrometry method in the clinical follow-up of a chronically infected patient over a 5-year period.     

Use of MALDI-TOF mass spectrometry in a 51-mutation test for cystic fibrosis: evidence that 3199del6 is a disease-causing mutation.

PURPOSE: We developed a 51-mutation extended cystic fibrosis (CF) panel that incorporates the 25 previously recommended CFTR mutations, plus 26 additional mutations including 3199del6, which was associated with I148T. METHODS: This assay utilizes an integrated matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry system. RESULTS: CF testing was performed on over 5,000 individuals, including a 3-year-old Hispanic-American patient with a compound heterozygous G542X/3199del6 genotype. He is negative for I148T, or other mutations assessed by CFTR gene sequencing. CONCLUSION: These results demonstrate the successful implementation of MALDI-TOF mass spectrometry in CF clinical testing, and establish 3199del6 as a disease-causing CF mutation.     

Androgen deficiency in women; role of accurate testosterone measurements

Androgen deficiency in women has been recognized as a distinct clinical syndrome that affects thousands of women particularly women in the postmenopausal period of their life. This syndrome has been described by several names including female androgen deficiency syndrome as well as hypoactive, sexual desire disorder. A recent large survey concerning sexual problems in women also adds personal distress as a potential contributor to the low sexual desire found in some women with sexual dysfunction. Recognition of an androgen deficiency syndrome however, has been controversial and limited to a clinical diagnosis due to the lack of accurate and sensitive methods for measuring androgens in women. Up until now, available methods for measuring the sex steroids have been dependent on antibody based assays that employ a range of different detection systems including the use of isotopes such as tritium and I-125 or chemical signalling molecules that produce chemiluminescence. These assays have become increasingly more sensitive for the measurement of testosterone but are still incapable of providing the proper low-end sensitivity for analyzing testosterone in female blood specimens. Assays for testosterone performed either manually or with highly automated immunoassay instruments have been used to measure testosterone in women but with varying degrees of success. Existing immunoassay-based methods are quite adequate for measuring testosterone levels in males but lack sufficient sensitivity to accurately and reproducibly measure testosterone in females and pre-pubertal children. Recent advances with the use of ultrasensitive methods such as mass spectrometry coupled to either gas or liquid chromatography have improved the technology for measuring testosterone and other low concentration sex steroids like estradiol to the degree that mass spectrometry based methods are now capable of measuring the testosterone levels found in normal women and in women with extremely low levels of testosterone as observed in a true androgen deficiency disorder. This application of mass spectrometry for measuring testosterone should allow clinicians to better define female androgen deficiency and facilitate further investigation in the diagnosis and optimal management of androgen deficiency in women.     

串联质谱技术在脂肪酸氧化代谢病诊断中的应用研究

目的探讨利用串联质谱技术检测干血滤纸片中酰基肉碱水平,诊断脂肪酸氧化代谢病。方法对象为2941例临床遗传性代谢病高危儿童,利用串联质谱技术检测患儿干血滤纸片中酰基肉碱水平,结合临床资料和常规生化结果,进行脂肪酸氧化代谢病诊断。结果诊断了14例脂肪酸氧化代谢病(0.5%),其中肉碱棕榈酰转移酶Ⅰ缺乏症1例,肉碱棕榈酰转移酶Ⅱ缺乏症1例,短链酰基辅酶A脱氢酶缺乏症1例,中链酰基辅酶A脱氢酶缺乏症7例,极长链酰基辅酶A脱氢酶缺乏症2例,多种酰基辅酶A脱氢酶缺乏症2例。结论通过串联质谱技术检测干血滤纸片中酰基肉碱水平,可对部分脂肪酸氧化代谢病进行诊断。     

Genetic and proteomic characterization of rifaximin resistance in Bifidobacterium infantis BI07

Rifaximin resistance in the probiotic strain Bifidobacterium infantis BI07 was studied to assess the use of an antibiotic-probiotic combination for clinical management of intestinal disorders. A rifaximin-resistant mutant was selected and a 129 bp core region of the rpoB gene was sequenced and compared with the respective sequence of the sensitive clone. A miss-sense mutation of codon 513, producing the substitution of Gln with Arg in the protein sequence, was found. The involvement of metabolic changes associated with rifaximin resistance was also investigated by proteomic analysis performed with two-dimensional electrophoresis and mass spectrometry. The principal categories of proteins, whose expression levels varied as a consequence of rifaximin resistance, included chaperonins, regulatory factors and metabolic enzymes. The hypothesis of rifaximin inactivation by bacterial enzymatic activities was excluded, as neither structural modifications nor degradation derivates of the drug moiety was identified using liquid chromatography coupled with tandem mass spectrometry.     

Matrix-assisted laser desorption ionization-time of flight mass spectrometry as an alternative to 16S rRNA gene sequencing for identification of difficult-to-identify bacterial strains

Conventional methods are sometimes insufficient to identify human bacterial pathogens, and alternative techniques, often molecular, are required. Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) identified with a valid score 45.9% of 410 clinical isolates from 207 different difficult-to-identify species having required 16S rRNA gene sequencing. MALDI-TOF MS might represent an alternative to 16S rRNA gene sequencing.     

Screening of beta-2 agonists and confirmation of fenoterol, orciprenaline, reproterol and terbutaline with gas chromatography-mass spectrometry as tetrahydroisoquinoline derivatives

A new method for a comprehensive screening and confirmation of beta-2 agonists in human urine is presented based on gas chromatography-low-resolution mass spectrometry (GC-MS) using electron impact ionisation (EI). After hydrolysis of the conjugates with beta-glucuronidase/arylsulfatase a derivatisation step with formaldehyde converts fenoterol, orciprenaline, reproterol and terbutaline to one derivative, a tetrahydroisoquinoline, while the other beta-2 agonists remain unchanged. Liquid-liquid extraction and trimethylsilylation follow. The tetrahydroisoquinoline derivatives show good gas chromatographic and mass spectrometric behaviour. The detection limit of these four beta-2 agonists in the screening using low-resolution mass spectrometry is 10 ng/ml of urine. The other beta-2 agonists are detected as parent compounds with the same recovery after sample preparation with and without formaldehyde. The EI mass spectra of the tetrahydroisoquinoline derivatives are presented.     

Quantitative detection of therapeutic proteins and their metabolites in serum using antibody-coupled ProteinChip Arrays and SELDI-TOF-MS

One of the important steps in developing protein therapeutics is the determination of their preliminary PK in vivo. These data are essential to design optimal dosing in animal models prior to progressing to clinical trials in man. The quantitative detection of protein therapeutics in serum is traditionally performed by ELISA, which has the prerequisite of the availability of the appropriate monoclonal antibodies. We have developed an alternative method using polyclonal antibodies immobilized on ProteinChip Arrays and SELDI-TOF mass spectrometry. This method has an advantage over ELISA since it provides simultaneously information on the clearance rate of the protein and it's in vivo processing. We compared these two methods using a RANTES variant, [(44)AANA(47)]-RANTES as the test protein in this study. Using SELDI-TOF mass spectrometry, we were able to establish that the protein is readily oxidized in serum, and moreover is processed in vivo to produce a truncated 3-68 protein, and undergoes a further cleavage to produce the 4-68 protein. These modifications are not identified by ELISA, whilst the serum exposure profiles determined by the two methods show essentially similar protein concentration values.     

Performance and cost analysis of matrix-assisted laser desorption ionization-time of flight mass spectrometry for routine identification of yeast

Matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry was compared to phenotypic testing for yeast identification. MALDI-TOF mass spectrometry yielded 96.3% and 84.5% accurate species level identifications (spectral scores, ≥ 1.8) for 138 common and 103 archived strains of yeast. MALDI-TOF mass spectrometry is accurate, rapid (5.1 min of hands-on time/identification), and cost-effective ($0.50/sample) for yeast identification in the clinical laboratory.     

质谱技术分析磷酸化蛋白的研究进展

蛋白质的可逆磷酸化是最重要的翻译后修饰之一,几乎参与生命活动的所有过程。虽然对于磷酸化蛋白的全面解析还存在巨大挑战,质谱已逐渐被人们认为是挑战这一领域的有利工具。质谱技术分析磷酸化蛋白质的方法包括利用抗体免疫沉淀、磷酸化蛋白胶染色、固定化的金属亲和层析柱、化学标签、强阳离子交换等技术富集磷酸化蛋白或肽段,串联质谱、电子俘获分析等技术检测磷酸化肽段并鉴定磷酸化位点,以及同位素标签对蛋白质磷酸化水平进行定量等。     

Proteomics in pathology research

Proteomics is a multifaceted approach to study various aspects of protein expression, post-translational modification, interactions, organization and function at a global level. While DNA constitutes the 'information archive of the genome', it is the proteins that actually serve as the functional effectors of cellular processes. Thus, analysis of protein derangements on a proteome-wide scale will reveal insights into deregulated pathways and networks involved in the pathogenesis of disease. Although the field of proteomics has advanced tremendously in recent years, there are significant technical challenges that pose limitations to the routine application of mass spectrometry to clinical research. Despite these challenges, proteomic studies have yielded unparalleled information and understanding of the cellular biology of diseased states. The application of mass spectrometry to the study of diseases will ultimately lead to identification of biomarkers that are critical for the detection, diagnosis, prognosis and treatment of specific disease entities.     

Measurement of carnitine precursors, epsilon-trimethyllysine and gamma-butyrobetaine in human serum by tandem mass spectrometry.

Methods using tandem mass spectrometry for measurement of epsilon-trimethyllysine and gamma-butyrobetaine in human serum are described. Precursor ion scan analysis of a methylated sample was applied for gamma-butyrobetaine measurement. However, for epsilon-trimethyllysine measurement, homoarginine interfered with the methylated sample during precursor ion scan analysis. To overcome this interference, the sample was propylated and acetylated prior to precursor ion scan analysis. The obtained values resembled those obtained by enzymatic or HPLC measurement. Using tandem mass spectrometry, all members of the carnitine family, free carnitine, acylcarnitines, gamma-butyrobetaine, epsilon-trimethyllysine can be analyzed in 0.1 ml of serum. Thus, the proposed method appears to be suitable for clinical application, especially in the pediatric field.     

DNA analysis by MALDI-TOF mass spectrometry

The last decade has seen an increased demand for high-throughput DNA analysis. This is mainly due to the human genome sequencing project that is now completed. Matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry was pinpointed early on as a technology that could be of great use for sequence variation analysis in the post-genome sequencing era. Applications developed first on this platform were for SNP genotyping. Several strategies for allele-discrimination (hybridization, cleavage, ligation, and primer extension) were combined with MALDI-TOF mass spectrometric detection. Nowadays, in practice, only primer extension methods are applied for large-scale SNP genotyping studies with MALDI-TOF detection. Problems surrounding the integration of SNP genotyping by MALDI-TOF mass spectrometry at high throughput are largely mastered now. Mass spectrometry geared presentations at the HUGO Mutation Detection Meeting in Palm Cove, Australia almost exclusively focused on novel applications that go beyond standard SNP genotyping. These applications are more demanding in terms of chemistry and molecular biology. Molecular haplotyping, expression profiling, DNA methylation analysis, and mutation detection are now being demonstrated.     

Biomedical mass spectrometry in today's and tomorrow's clinical microbiology laboratories

Clinical microbiology is a conservative laboratory exercise where base technologies introduced in the 19th century remained essentially unaltered. High-tech mass spectrometry (MS) has changed that. Within a few years following its adaptation to microbiological diagnostics, MS has been introduced, embraced, and broadly accepted by clinical microbiology laboratories throughout the world as an innovative tool for definitive bacterial species identification. Herein, we review the current state of the art with respect to this exciting new technology and discuss potential future applications.