The importance of the digest: proteolysis and absolute quantification in proteomics

Virtually all mass spectrometric-based methods for quantitative proteomics are at the peptide level, whether label-mediated or label-free. Absolute quantification in particular is based on the measurement of limit peptides, defined as those peptides that cannot be further fragmented by the protease in use. Complete release of analyte and (stable isotope labelled) standard ensures that the most reliable quantification data are recovered, especially when the standard peptides are in a different primary sequence context, such as sometimes occurs in the QconCAT methodology. Moreover, in label-free methods, incomplete digestion would diminish the ion current attributable to limit peptides and lead to artifactually low quantification data. It follows that an essential requirement for peptide-based absolute quantification in proteomics is complete and consistent proteolysis to limit peptides. In this paper we describe strategies to assess completeness of proteolysis and discuss the potential for variance in digestion efficiency to compromise the ensuing quantification data. We examine the potential for kinetically favoured routes of proteolysis, particularly at the last stages of the digestion, to direct products into ‘dead-end’ mis-cleaved products.     

Development of selected reaction monitoring‐MS methodology to measure peptide biomarkers in prostate cancer

Prostate cancer is a leading cause of cancer‐related death. The current modality of diagnosis, the measurement of serum PSA, not only suffers from lack of specificity, but does not distinguish clinical cases in which current treatment measures would be most successful, i.e. aggressive, life‐threatening tumors. A multiplexed MS methodology, selected reaction monitoring‐MS/MS coupled with stable isotope dilution (SID), was developed and tested in both cells lines and clinical tissue samples. Standard curves were generated for two peptides representing PSA and one peptide from each of two additional orthogonally validated biomarkers, AMACR and EZH2. The standard curves show high reproducibility, sensitivity, and good linearity. All four peptides were then measured in six clinically relevant cell lines and are in agreement with the biochemical characteristics of each individual cell line. The SID selected reaction monitoring‐MS/MS methodology was then transferred to tissue samples, in which the assay shows potential to differentiate benign disease from localized cancer and localized cancer from aggressive metastatic disease. These results establish the preliminary development of a rational targeted MS platform that strives to bridge the gap between discovery and validation of biomarkers for the detection of prostate cancer.     

Flow injection analysis electrospray ionization mass spectrometry for high-throughput screening of a gene library for amidase activity

In high-throughput screening of gene and mutant libraries, high analysis speeds and short method development times are important factors. Mass spectrometry (MS) is considered to be a generic analytical technique with a relatively short development time. Furthermore, when applying flow injection analysis (FIA) for sample introduction, the requirements for high throughput are met. In this work, the use of a single quadrupole electrospray MS instrument for assaying amidase activity in a gene library is demonstrated. The desired selectivity for measuring the amino acid, the reaction product of the amidase reaction, in the presence of high concentrations of the corresponding amino acid amide substrate was obtained by selective ionization of the amino acid in negative ion mode electrospray. The only sample preparation required was a 200-fold dilution of the reaction mixture. For obtaining quantitative results, a complementary calibration procedure was set up to correct for the change in ionization suppression as a function of conversion. This approach was used to screen a Mycobacterium neoaurum gene library consisting of 11,520 clones with α-methylleucine amide as substrate within 24 h. Conversion was measured on the [M−H]⁻ species of the corresponding α-methylleucine (m/z 144). Five positive clones were detected with a conversion ranging from 0.2% to 3.4%.     

Myeloperoxidase targets apolipoprotein A-I, the major high density lipoprotein protein, for site-specific oxidation in human atherosclerotic lesions

Oxidative damage by myeloperoxidase (MPO) has been proposed to deprive HDL of its cardioprotective effects. In vitro studies reveal that MPO chlorinates and nitrates specific tyrosine residues of apoA-I, the major HDL protein. After Tyr-192 is chlorinated, apoA-I is less able to promote cholesterol efflux by the ABCA1 pathway. To investigate the potential role of this pathway in vivo, we used tandem mass spectrometry with selected reaction monitoring to quantify the regiospecific oxidation of apoA-I. This approach demonstrated that Tyr-192 is the major chlorination site in apoA-I in both plasma and lesion HDL of humans. We also found that Tyr-192 is the major nitration site in apoA-I of circulating HDL but that Tyr-18 is the major site in lesion HDL. Levels of 3-nitrotyrosine strongly correlated with levels of 3-chlorotyrosine in lesion HDL, and Tyr-18 of apoA-I was the major nitration site in HDL exposed to MPO in vitro, suggesting that MPO is the major pathway for chlorination and nitration of HDL in human atherosclerotic tissue. These observations may have implications for treating cardiovascular disease, because recombinant apoA-I is under investigation as a therapeutic agent and mutant forms of apoA-I that resist oxidation might be more cardioprotective than the native form.     

基于水稻产量构成性状间相关性的选种标准数学模型建立

选用54个水稻杂交组合F1代,对穗粒数、有效穗数、千粒重、穗谷重等产量构成性状进行相关、回归分析及其线性方程相交分析,并建立水稻选种入选标准的数学模型.结果表明:穗粒数(X_1)分别与其它三个性状间的相关达极显著水平,这四个性状的复相关系数达到极显著水平,表现为水稻产量构成性状间是互相影响、互为矛盾,构成性状间的矛盾与统一;经标准化的有效穗数(X_2)、千粒重(X_3)和穗谷重(X_4)分别依穗粒数(X_1)回归的线性回归方程分别为,x_2=0.6797-0.5907x_1,x_3=0.7268-0.4917x_1,x_4=0.2466+0.5053x_1.根据这些方程的升降性,分别组成联立方程组,求出这四个数量性状互作的矛盾统一点为:穗粒数136.6粒、有效穗数7.72穗/丛、千粒重23.53g、穗谷重3.09g;这四个性状相互作用、相互协调的优良表现型值落在穗粒数为132.3-177.0粒范围内.以穗粒数、有效穗数、千粒重、穗谷重的线性关系,建立的水稻选种入选标准数学模型具有较好的预见性和实用性.     

Detection of volatile compounds produced by microbial growth in urine by selected ion flow tube mass spectrometry (SIFT-MS)

Selected ion flow tube-mass spectrometry has been used to measure the volatile compounds occurring in the headspace of urine samples inoculated with common urinary tract infection (UTI)-causing microbes Escherichia coli, Proteus vulgaris, Pseudomonas aeruginosa, Staphylococcus aureus, Staphylococcus epidermidis, Klebsiella pneumoniae, Enterococcus faecalis, or Candida albicans. This technique has the potential to offer rapid and simple diagnosis of the causative agent of UTIs.     

Identification of a seven glycopeptide signature for malignant pleural mesothelioma in human serum by selected reaction monitoring

Background

Serum biomarkers can improve diagnosis and treatment of malignant pleural mesothelioma (MPM). However, the evaluation of potential new serum biomarker candidates is hampered by a lack of assay technologies for their clinical evaluation. Here we followed a hypothesis-driven targeted proteomics strategy for the identification and clinical evaluation of MPM candidate biomarkers in serum of patient cohorts.

Results

Based on the hypothesis that cell surface exposed glycoproteins are prone to be released from tumor-cells to the circulatory system, we screened the surfaceome of model cell lines for potential MPM candidate biomarkers. Selected Reaction Monitoring (SRM) assay technology allowed for the direct evaluation of the newly identified candidates in serum. Our evaluation of 51 candidate biomarkers in the context of a training and an independent validation set revealed a reproducible glycopeptide signature of MPM in serum which complemented the MPM biomarker mesothelin.

Conclusions

Our study shows that SRM assay technology enables the direct clinical evaluation of protein-derived candidate biomarker panels for which clinically reliable ELISA’s currently do not exist.     

Quantitative analysis of glycosaminoglycans,chondroitin/dermatan sulfate,hyaluronic acid,heparan sulfate,and keratan sulfate by liquid chromatography–electrospray ionization–tandem mass spectrometry

We developed a method using liquid chromatography–electrospray ionization–tandem mass spectrometry (LC–ESI–MS/MS) with a selected reaction monitoring (SRM) mode for simultaneous quantitative analysis of glycosaminoglycans (GAGs). Using one-shot analysis with our MS/MS method, we demonstrated the simultaneous quantification of a total of 23 variously sulfated disaccharides of four GAG classes (8 chondroitin/dermatan sulfates, 1 hyaluronic acid, 12 heparan sulfates, and 2 keratan sulfates) with a sensitivity of less than 0.5 pmol within 20 min. We showed the differences in the composition of GAG classes and the sulfation patterns between porcine articular cartilage and yellow ligament. In addition to the internal disaccharides described above, some saccharides derived from the nonreducing terminal were detected simultaneously. The simultaneous quantification of both internal and nonreducing terminal saccharides could be useful to estimate the chain length of GAGs. This method would help to establish comprehensive “GAGomic” analysis of biological tissues.