Liquid MALDI MS analysis of complex peptide and proteome samples

Matrix-assisted laser desorption/ionization (MALDI) time-of-flight (TOF) mass spectrometry (MS) is well-known to be a powerful technique for the analysis of biological samples. By using glycerol-based liquid support matrices (LSMs) instead of conventional MALDI matrices the power of this technique can be extended further. In this study, we exploited LSMs for the identification of complex samples, i.e. the Lactobacillus proteome and a bovine serum albumin (BSA) digest. Liquid and solid MALDI samples were manually and robotically prepared by coupling a nanoflow high performance liquid chromatography (nanoHPLC) system to an automated MALDI sample spotting device. MS and MS/MS data were successfully acquired at the femtomole level using TOF/TOF as well as Q-TOF instrumentation and used for protein identification searching sequence databases. For the BSA digest analysis, liquid MALDI samples resulted in peptide mass fingerprints which led to a higher confidence in protein identification compared to solid (crystalline) MALDI samples. However, post-source decay (PSD) MS/MS analysis of both the proteome of Lactobacillus plantarum WCFS1 cells and BSA digest showed that further optimization of the formation and detection of peptide fragment ions is still needed for liquid MALDI samples as the MS/MS ion search score was lower than for the solid MALDI samples, reflecting the poorer quality of the liquid MALDI-PSD spectra, which can be attributed to the differences in PSD parameters and their optimization that is currently achievable

Sample preparation: a crucial factor for the analytical performance of rationally designed MALDI matrices

Evidence is presented that the performance of the rationally designed MALDI matrix 4-chloro-α-cyanocinnamic acid (ClCCA) in comparison to its well-established predecessor α-cyano-4-hydroxycinnamic acid (CHCA) is significantly dependent on the sample preparation, such as the choice of the target plate. In this context, it becomes clear that any rational designs of MALDI matrices and their successful employment have to consider a larger set of physicochemical parameters, including sample crystallization and morphology/topology, in addition to parameters of basic (solution and/or gas-phase) chemistry

Protein identification using a nanoUHPLC-AP-MALDI MS/MS workflow with CID of multiply charged proteolytic peptides

Liquid AP-MALDI can produce predominantly multiply charged ESI-like ions and stable durable analyte ion yields with samples allowing good shot-to-shot reproducibility and exhibiting self-healing properties during laser irradiation. In this study, LC-MALDI MS/MS workflows that utilize multiply charged ions are reported for the first time and compared with standard LC-ESI MS/MS for bottom-up proteomic analysis. The proposed method is compatible with trifluoroacetic acid as an LC ion pairing reagent and allows multiple MS/MS acquisitions of the LC-separated samples without substantial sample consumption. In addition, the method facilitates the storage of fully spotted MALDI target plates for months without significant sample degradation

Optimizing outcomes for children with non-Hodgkin lymphoma in low- and middle-income countries by early correct diagnosis, reducing toxic death and preventing abandonment

In high-income countries, more than 90% of children with mature B-cell lymphomas are cured with frontline therapy. However, cure requires prompt and correct diagnosis, careful risk stratification, very intense chemotherapy and meticulous supportive care, together with logistical support for patients who live far from the cancer centre or face financial barriers to receiving care. In low- and middle-income countries (LMIC), cure rates range from 20% to 70% because of lack of diagnosis, misdiagnosis, abandonment of treatment, toxic death and excess relapse with reduced-intensity regimens. Fortunately, a wide range of successful interventions in LMIC have reduced these causes of avoidable treatment failure. Public awareness campaigns have led to societal awareness of childhood cancer; telepathology has improved diagnosis, even in remote areas; subsidized chemotherapy, transportation, housing and food have reduced abandonment; and hand hygiene, nurse training programmes and health system improvements have reduced toxic death. These interventions can be deployed everywhere and at low cost, so are highly scalable. Children and adolescents with Burkitt lymphoma can be cured in all countries by making a timely correct diagnosis, applying protocols adapted to the local context, preventing abandonment of therapy and avoiding toxic death. Reducing these causes of treatment failure is feasible and highly cost-effective everywhere.Fil: Chantada, Guillermo Luis. Hospital Universitario Austral; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Lam, Catherine G.. St. Jude Children's Research Hospital; Estados UnidosFil: Howard, Scott C.. University of Tennessee; Estados Unido

Global surveillance of cancer survival 1995-2009: analysis of individual data for 25,676,887 patients from 279 population-based registries in 67 countries (CONCORD-2)

BACKGROUND: Worldwide data for cancer survival are scarce. We aimed to initiate worldwide surveillance of cancer survival by central analysis of population-based registry data, as a metric of the effectiveness of health systems, and to inform global policy on cancer control. METHODS: Individual tumour records were submitted by 279 population-based cancer registries in 67 countries for 25·7 million adults (age 15-99 years) and 75,000 children (age 0-14 years) diagnosed with cancer during 1995-2009 and followed up to Dec 31, 2009, or later. We looked at cancers of the stomach, colon, rectum, liver, lung, breast (women), cervix, ovary, and prostate in adults, and adult and childhood leukaemia. Standardised quality control procedures were applied; errors were corrected by the registry concerned. We estimated 5-year net survival, adjusted for background mortality in every country or region by age (single year), sex, and calendar year, and by race or ethnic origin in some countries. Estimates were age-standardised with the International Cancer Survival Standard weights. FINDINGS: 5-year survival from colon, rectal, and breast cancers has increased steadily in most developed countries. For patients diagnosed during 2005-09, survival for colon and rectal cancer reached 60% or more in 22 countries around the world; for breast cancer, 5-year survival rose to 85% or higher in 17 countries worldwide. Liver and lung cancer remain lethal in all nations: for both cancers, 5-year survival is below 20% everywhere in Europe, in the range 15-19% in North America, and as low as 7-9% in Mongolia and Thailand. Striking rises in 5-year survival from prostate cancer have occurred in many countries: survival rose by 10-20% between 1995-99 and 2005-09 in 22 countries in South America, Asia, and Europe, but survival still varies widely around the world, from less than 60% in Bulgaria and Thailand to 95% or more in Brazil, Puerto Rico, and the USA. For cervical cancer, national estimates of 5-year survival range from less than 50% to more than 70%; regional variations are much wider, and improvements between 1995-99 and 2005-09 have generally been slight. For women diagnosed with ovarian cancer in 2005-09, 5-year survival was 40% or higher only in Ecuador, the USA, and 17 countries in Asia and Europe. 5-year survival for stomach cancer in 2005-09 was high (54-58%) in Japan and South Korea, compared with less than 40% in other countries. By contrast, 5-year survival from adult leukaemia in Japan and South Korea (18-23%) is lower than in most other countries. 5-year survival from childhood acute lymphoblastic leukaemia is less than 60% in several countries, but as high as 90% in Canada and four European countries, which suggests major deficiencies in the management of a largely curable disease. INTERPRETATION: International comparison of survival trends reveals very wide differences that are likely to be attributable to differences in access to early diagnosis and optimum treatment. Continuous worldwide surveillance of cancer survival should become an indispensable source of information for cancer patients and researchers and a stimulus for politicians to improve health policy and health-care systems

Worldwide comparison of survival from childhood leukaemia for 1995–2009, by subtype, age, and sex (CONCORD-2): a population-based study of individual data for 89 828 children from 198 registries in 53 countries

Background Global inequalities in access to health care are reflected in differences in cancer survival. The CONCORD programme was designed to assess worldwide differences and trends in population-based cancer survival. In this population-based study, we aimed to estimate survival inequalities globally for several subtypes of childhood leukaemia. Methods Cancer registries participating in CONCORD were asked to submit tumour registrations for all children aged 0-14 years who were diagnosed with leukaemia between Jan 1, 1995, and Dec 31, 2009, and followed up until Dec 31, 2009. Haematological malignancies were defined by morphology codes in the International Classification of Diseases for Oncology, third revision. We excluded data from registries from which the data were judged to be less reliable, or included only lymphomas, and data from countries in which data for fewer than ten children were available for analysis. We also excluded records because of a missing date of birth, diagnosis, or last known vital status. We estimated 5-year net survival (ie, the probability of surviving at least 5 years after diagnosis, after controlling for deaths from other causes [background mortality]) for children by calendar period of diagnosis (1995-99, 2000-04, and 2005-09), sex, and age at diagnosis (< 1, 1-4, 5-9, and 10-14 years, inclusive) using appropriate life tables. We estimated age-standardised net survival for international comparison of survival trends for precursor-cell acute lymphoblastic leukaemia (ALL) and acute myeloid leukaemia (AML). Findings We analysed data from 89 828 children from 198 registries in 53 countries. During 1995-99, 5-year agestandardised net survival for all lymphoid leukaemias combined ranged from 10.6% (95% CI 3.1-18.2) in the Chinese registries to 86.8% (81.6-92.0) in Austria. International differences in 5-year survival for childhood leukaemia were still large as recently as 2005-09, when age-standardised survival for lymphoid leukaemias ranged from 52.4% (95% CI 42.8-61.9) in Cali, Colombia, to 91.6% (89.5-93.6) in the German registries, and for AML ranged from 33.3% (18.9-47.7) in Bulgaria to 78.2% (72.0-84.3) in German registries. Survival from precursor-cell ALL was very close to that of all lymphoid leukaemias combined, with similar variation. In most countries, survival from AML improved more than survival from ALL between 2000-04 and 2005-09. Survival for each type of leukaemia varied markedly with age: survival was highest for children aged 1-4 and 5-9 years, and lowest for infants (younger than 1 year). There was no systematic difference in survival between boys and girls. Interpretation Global inequalities in survival from childhood leukaemia have narrowed with time but remain very wide for both ALL and AML. These results provide useful information for health policy makers on the effectiveness of health-care systems and for cancer policy makers to reduce inequalities in childhood survival

Childhood cancer incidence and survival in Thailand: A comprehensive population‐based registry analysis, 1990–2011

BackgroundSoutheast Asia is undergoing a transition from infectious to chronic diseases, including a dramatic increase in adult cancers. Childhood cancer research in Thailand has focused predominantly on leukemias and lymphomas or only examined children for a short period of time. This comprehensive multisite study examined childhood cancer incidence and survival rates in Thailand across all International Classification of Childhood Cancer (ICCC) groups over a 20‐year period.MethodsCancer cases diagnosed in children ages 0‐19 years (n = 3574) from 1990 to 2011 were extracted from five provincial population‐based Thai registries, covering approximately 10% of the population. Descriptive statistics of the quality of the registries were evaluated. Age‐standardized incidence rates (ASRs) were calculated using the Segi world standard population, and relative survival was computed using the Kaplan‐Meier method. Changes in incidence and survival were analyzed using Joinpoint Regression and reported as annual percent changes (APC).ResultsThe ASR of all childhood cancers during the study period was 98.5 per million person‐years with 91.0 per million person‐years in 1990–2000 and 106.2 per million person‐years in 2001–2011. Incidence of all childhood cancers increased significantly (APC = 1.2%, P < 0.01). The top three cancer groups were leukemias, brain tumors, and lymphomas. The 5‐year survival for all childhood cancers significantly improved from 39.4% in 1990–2000 to 47.2% in 2001–2011 (P < 0.01).ConclusionsBoth childhood cancer incidence and survival rates have increased, suggesting improvement in the health care system as more cases are identified and treated. Analyzing childhood cancer trends in low‐ and middle‐income countries can improve understanding of cancer etiology and pediatric health care disparities.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/146559/1/pbc27428_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/146559/2/pbc27428.pd

Detection of monoclonal immunoglobulin heavy chain gene rearrangement (FR3) in Thai malignant lymphoma by High Resolution Melting curve analysis

<p>Abstract</p> <p>Malignant lymphoma, especially non-Hodgkin lymphoma, is one of the most common hematologic malignancies in Thailand. The diagnosis of malignant lymphoma is often problematic, especially in early stages of the disease. Detection of antigen receptor gene rearrangement including T cell receptor (TCR) and immunoglobulin heavy chain (IgH) by polymerase chain reaction followed by heteroduplex has currently become standard whereas fluorescent fragment analysis (GeneScan) has been used for confirmation test. In this study, three techniques had been compared: thermocycler polymerase chain reaction (PCR) followed by heteroduplex and polyacrylamide gel electrophoresis, GeneScan analysis, and real time PCR with High Resolution Melting curve analysis (HRM). The comparison was carried out with DNA extracted from paraffin embedded tissues diagnosed as B- cell non-Hodgkin lymphoma. Specific PCR primers sequences for IgH gene variable region 3, including fluorescence labeled IgH primers were used and results were compared with HRM. In conclusion, the detection IgH gene rearrangement by HRM in the LightCycler System showed potential for distinguishing monoclonality from polyclonality in B-cell non-Hodgkin lymphoma.</p> <p>Introduction</p> <p>Malignant lymphoma, especially non-Hodgkin lymphoma, is one of the most common hematologic malignancies in Thailand. The incidence rate as reported by Ministry of Public Health is 3.1 per 100,000 population in female whereas the rate in male is 4.5 per 100,000 population <abbrgrp><abbr bid="B1">1</abbr></abbrgrp>. At Siriraj Hospital, the new cases diagnosed as malignant lymphoma were 214.6 cases/year <abbrgrp><abbr bid="B2">2</abbr></abbrgrp>. The diagnosis of malignant lymphoma is often problematic, especially in early stages of the disease. Therefore, detection of antigen receptor gene rearrangement including T cell receptor (TCR) and immunoglobulin heavy chain (IgH) by polymerase chain reaction (PCR) assay has recently become a standard laboratory test for discrimination of reactive from malignant clonal lymphoproliferation <abbrgrp><abbr bid="B3">3</abbr><abbr bid="B4">4</abbr></abbrgrp>. Analyzing DNA extracted from formalin-fixed, paraffin-embedded tissues by multiplex PCR techniques is more rapid, accurate and highly sensitive. Measuring the size of the amplicon from PCR analysis could be used to diagnose malignant lymphoma with monoclonal pattern showing specific and distinct bands detected on acrylamide gel electrophoresis. However, this technique has some limitations and some patients might require a further confirmation test such as GeneScan or fragment analysis <abbrgrp><abbr bid="B5">5</abbr><abbr bid="B6">6</abbr></abbrgrp>.</p> <p>GeneScan technique or fragment analysis reflects size and peak of DNA by using capillary gel electrophoresis. This technique is highly sensitive and can detect 0.5-1% of clonal lymphoid cells. It measures the amplicons by using various fluorescently labeled primers at forward or reverse sides and a specific size standard. Using a Genetic Analyzer machine and GeneMapper software (Applied Bioscience, USA), the monoclonal pattern revealed one single, sharp and high peak at the specific size corresponding to acrylamide gel pattern, whereas the polyclonal pattern showed multiple and small peak condensed at the same size standard. This technique is the most sensitive and accurate technique; however, it usually requires high technical experience and is also of high cost <abbrgrp><abbr bid="B7">7</abbr></abbrgrp>. Therefore, rapid and more cost effective technique are being sought.</p> <p>LightCycler PCR performs the diagnostic detection of amplicon via melting curve analysis within 2 hours with the use of a specific dye <abbrgrp><abbr bid="B8">8</abbr><abbr bid="B9">9</abbr></abbrgrp>. This dye consists of two types: one known as SYBR-Green I which is non specific and the other named as High Resolution Melting analysis (HRM) which is highly sensitive, more accurate and stable. Several reports demonstrated that this new instrument combined with DNA intercalating dyes can be used to discriminate sequence changes in PCR amplicon without manual handling of PCR product <abbrgrp><abbr bid="B10">10</abbr><abbr bid="B11">11</abbr></abbrgrp>. Therefore, current investigations using melting curve analysis are being developed <abbrgrp><abbr bid="B12">12</abbr><abbr bid="B13">13</abbr></abbrgrp>.</p> <p>In this study, three different techniques were compared to evaluate the suitability of LightCycler PCR with HRM as the clonal diagnostic tool for IgH gene rearrangement in B-cell non-Hogdkin lymphoma, i.e. thermocycler PCR followed by heteroduplex analysis and PAGE, GeneScan analysis and LightCycler PCR with HRM.</p

CCQM-K55.b (Aldrin) : Final report: october 2012. CCQM-K55.b key comparison on the characterization of organic substances for chemical purity

Under the auspices of the Organic Analysis Working Group (OAWG) of the Comité Consultatif pour la Quantité de Matière (CCQM) a key comparison, CCQM K55.b, was coordinated by the Bureau International des Poids et Mesures (BIPM) in 2010/2011. Nineteen national measurement institutes and the BIPM participated. Participants were required to assign the mass fraction of aldrin present as the main component in the comparison sample for CCQM-K55.b which consisted of technical grade aldrin obtained from the National Measurement Institute Australia that had been subject to serial recrystallization and drying prior to sub-division into the units supplied for the comparison. Aldrin was selected to be representative of the performance of a laboratory's measurement capability for the purity assignment of organic compounds of medium structural complexity [molar mass range 300 Da to 500 Da] and low polarity (pKOW < −2) for which related structure impurities can be quantified by capillary gas phase chromatography (GC). The key comparison reference value (KCRV) for the aldrin content of the material was 950.8 mg/g with a combined standard uncertainty of 0.85 mg/g. The KCRV was assigned by combination of KCRVs assigned by consensus from participant results for each orthogonal impurity class. The relative expanded uncertainties reported by laboratories having results consistent with the KCRV ranged from 0.3% to 0.6% using a mass balance approach and 0.5% to 1% using a qNMR method. The major analytical challenge posed by the material proved to be the detection and quantification of a significant amount of oligomeric organic material within the sample and most participants relying on a mass balance approach displayed a positive bias relative to the KCRV (overestimation of aldrin content) in excess of 10 mg/g due to not having adequate procedures in place to detect and quantify the non-volatile content—specifically the non-volatile organics content—of the comparison sample. There was in general excellent agreement between participants in the identification and the quantification of the total and individual related structure impurities, water content and the residual solvent content of the sample. The comparison demonstrated the utility of 1H NMR as an independent method for quantitative analysis of high purity compounds. In discussion of the participant results it was noted that while several had access to qNMR estimates for the aldrin content that were inconsistent with their mass balance determination they decided to accept the mass balance result and assumed a hidden bias in their NMR data. By contrast, laboratories that placed greater confidence in their qNMR result were able to resolve the discrepancy through additional studies that provided evidence of the presence of non-volatile organic impurity at the requisite level to bring their mass balance and qNMR estimates into agreement.Fil: Westwood, Steven. Bureau International des Poids et Mesures (BIPM); FranciaFil: Josephs, Ralf. Bureau International des Poids et Mesures (BIPM); FranciaFil: Choteau, Tiphaine. Bureau International des Poids et Mesures (BIPM); FranciaFil: Daireaux, Adeline. Bureau International des Poids et Mesures (BIPM); FranciaFil: Mesquida, Charline. Bureau International des Poids et Mesures (BIPM); FranciaFil: Wielgosz, Robert. Bureau International des Poids et Mesures (BIPM); FranciaFil: Rosso, Adriana. Instituto Nacional de Tecnología Industrial (INTI); ArgentinaFil: Ruiz de Arechavaleta, Mariana. Instituto Nacional de Tecnología Industrial (INTI); ArgentinaFil: Davies, Stephen. National Measurement Institute (NMIA); AustraliaFil: Wang, Hongjie. National Measurement Institute (NMIA); AustraliaFil: Pires do Rego, Eliane Cristina. Instituto Nacional de Metrologia, Qualidade e Tecnologia (INMetro); BrasilFil: Marques Rodrigues, Janaína. Instituto Nacional de Metrologia, Qualidade e Tecnologia (INMetro); BrasilFil: de Freitas Guimarães, Evelyn. Instituto Nacional de Metrologia, Qualidade e Tecnologia (INMetro); BrasilFil: Barreto Sousa, Marcus Vinicius. Instituto Nacional de Metrologia, Qualidade e Tecnologia (INMetro); BrasilFil: Monteiro, Tânia Maria. Instituto Nacional de Metrologia, Qualidade e Tecnologia (INMetro); BrasilFil: Alves das Neves Valente, Laura. Instituto Nacional de Metrologia, Qualidade e Tecnologia (INMetro); BrasilFil: Marques Violante, Fernando Gustavo. Instituto Nacional de Metrologia, Qualidade e Tecnologia (INMetro); BrasilFil: Rubim, Renato. Instituto Nacional de Metrologia, Qualidade e Tecnologia (INMetro); BrasilFil: Almeida, Ribeiro. Instituto Nacional de Metrologia, Qualidade e Tecnologia (INMetro); BrasilFil: Baptista Quaresma, Maria Cristina. Instituto Nacional de Metrologia, Qualidade e Tecnologia (INMetro); BrasilFil: Nogueira, Raquel. Instituto Nacional de Metrologia, Qualidade e Tecnologia (INMetro); BrasilFil: Windust, Anthony. Institute for National Measurement Standards. National Research Council Canada (NRC-INMS); CanadáFil: Dai, Xinhua. National Institute of Metrology (NIM); ChinaFil: Li, Xiaomin. National Institute of Metrology (NIM); ChinaFil: Zhang, Wei. National Institute of Metrology (NIM); ChinaFil: Li, Ming. National Institute of Metrology (NIM); ChinaFil: Shao, Mingwu. National Institute of Metrology (NIM); ChinaFil: Wei, Chao. National Institute of Metrology (NIM); ChinaFil: Wong, Siu-kay. Government Laboratory of Hong Kong SAR (GLHK); ChinaFil: Cabillic, Julie. Laboratoire National de Métrologie et d’Essais (LNE); FranciaFil: Gantois, Fanny. Laboratoire National de Métrologie et d’Essais (LNE); FranciaFil: Philipp, Rosemarie. Bundesanstalt für Materialforschung (BAM); AlemaniaFil: Pfeifer, Dietmar. Bundesanstalt für Materialforschung (BAM); AlemaniaFil: Hein, Sebastian. Bundesanstalt für Materialforschung (BAM); AlemaniaFil: Klyk-Seitz, Urszula-Anna. Bundesanstalt für Materialforschung (BAM); AlemaniaFil: Ishikawa, Keiichiro. National Metrology Institute of Japan (NMIJ); JapónFil: Castro, Esther. Centro Nacional de Metrología (CENAM); MéxicoFil: Gonzalez, Norma. Centro Nacional de Metrología (CENAM); MéxicoFil: Krylov, Anatoly. D. I. Mendeleev Institute for Metrology (VNIIM); RusiaFil: Lin, Teo Tang. Health Sciences Authority (HSA); SingapurFil: Kooi, Lee Tong. Health Sciences Authority (HSA); SingapurFil: Fernandes-Whaley, M. National Metrology Institute of South Africa (NMISA); SudáfricaFil: Prévoo, D. National Metrology Institute of South Africa (NMISA); SudáfricaFil: Archer, M. National Metrology Institute of South Africa (NMISA); SudáfricaFil: Visser, R. National Metrology Institute of South Africa (NMISA); SudáfricaFil: Nlhapo, N. National Metrology Institute of South Africa (NMISA); SudáfricaFil: de Vos, B. National Metrology Institute of South Africa (NMISA); SudáfricaFil: Ahn, Seonghee. Korea Research Institute of Standards and Science (KRISS); Corea del SurFil: Pookrod, Preeyaporn. National Institute of Metrology of Thailand (NIMT); TailandiaFil: Wiangnon, Kanjana. National Institute of Metrology of Thailand (NIMT); TailandiaFil: Sudsiri, Nittaya. National Institute of Metrology of Thailand (NIMT); TailandiaFil: Muaksang, Kittiya. National Institute of Metrology of Thailand (NIMT); TailandiaFil: Cherdchu, Chainarong. National Institute of Metrology of Thailand (NIMT); TailandiaFil: Gören, Ahmet Ceyhan. National Metrology Institute (TUBITAK UME); TurquíaFil: Bilsel, Mine. National Metrology Institute (TUBITAK UME); TurquíaFil: LeGoff, Thierry. LGC Limited; Reino UnidoFil: Bearden, Dan. National Institute of Standards and Technology (NIST); Estados UnidosFil: Bedner, Mary. National Institute of Standards and Technology (NIST); Estados UnidosFil: Duewer, David. National Institute of Standards and Technology (NIST); Estados UnidosFil: Hancock, Diane. National Institute of Standards and Technology (NIST); Estados UnidosFil: Lang, Brian. National Institute of Standards and Technology (NIST); Estados UnidosFil: Lippa, Katrice. National Institute of Standards and Technology (NIST); Estados UnidosFil: Schantz, Michele. National Institute of Standards and Technology (NIST); Estados UnidosFil: Sieber, John. National Institute of Standards and Technology (NIST); Estados Unido