RESUMO
We sought to develop a safe and effective outpatient salvage regimen by replacing ifosfamide within the (R)ICE (rituximab, ifosfomide, carboplatin, etoposide) regimen with bendamustine (T(R)EC) via a multicentre phase I/II study for patients with relapsed or refractory diffuse large B cell lymphoma (DLBCL) and classic Hodgkin lymphoma (HL). Therapy consisted of 60-120 mg/m2 per day bendamustine on days 1 and 2 in combination with carboplatin, etoposide and rituximab (only for CD20+ lymphoma) used in the (R)ICE regimen for up to 2 cycles. The objectives were to define a maximally tolerated dose (MTD) of bendamustine, determine safety and toxicity, assess efficacy, and evaluate impact on stem cell collection. Forty-eight patients were treated of which 71% had refractory disease. No dose-limiting toxicities were observed. The recommended phase II dose of bendamustine was 120 mg/m2 per day on days 1 and 2. Response rates were 85% (70% complete response, CR) in HL, and 65% (40% CR) in DLBCL. Stem cell collection was successful in 30 of 32 patients. The most common non-haematological toxicities ≥grade 3 were febrile neutropenia (8%) and dehydration (8%). The T(R)EC regimen safely yields high response rates, successfully mobilizes peripheral blood stem cells and compares favourably to RICE, offering an effective outpatient treatment option for patients with relapsed or refractory DLBCL and HL.
Assuntos
Protocolos de Quimioterapia Combinada Antineoplásica/administração & dosagem , Linfoma Difuso de Grandes Células B/tratamento farmacológico , Adulto , Idoso , Protocolos de Quimioterapia Combinada Antineoplásica/efeitos adversos , Cloridrato de Bendamustina/administração & dosagem , Cloridrato de Bendamustina/efeitos adversos , Carboplatina/administração & dosagem , Carboplatina/efeitos adversos , Desidratação/induzido quimicamente , Desidratação/epidemiologia , Etoposídeo/administração & dosagem , Etoposídeo/efeitos adversos , Neutropenia Febril/induzido quimicamente , Neutropenia Febril/epidemiologia , Feminino , Humanos , Linfoma Difuso de Grandes Células B/epidemiologia , Masculino , Pessoa de Meia-Idade , Estudos Prospectivos , Recidiva , Rituximab/administração & dosagem , Rituximab/efeitos adversosAssuntos
Anemia Hemolítica Autoimune/etiologia , Leucemia Linfocítica Crônica de Células B/complicações , Aplasia Pura de Série Vermelha/etiologia , Adenina/efeitos adversos , Adenina/análogos & derivados , Adenina/uso terapêutico , Idoso , Anemia Hemolítica Autoimune/complicações , Antineoplásicos/efeitos adversos , Antineoplásicos/uso terapêutico , Humanos , Leucemia Linfocítica Crônica de Células B/tratamento farmacológico , Leucemia Linfocítica Crônica de Células B/patologia , Masculino , Piperidinas/efeitos adversos , Piperidinas/uso terapêutico , Aplasia Pura de Série Vermelha/complicações , Esteroides/uso terapêutico , Viroses/genéticaRESUMO
Conversion to the International Classification of Diseases, 10th Revision, Clinical Modification (ICD-10-CM) was mandated for October 1, 2014, but was delayed by one year. ICD-10 accommodates newly developed diagnoses and procedures and is expected to help measure quality of care. When implemented, it will impact oncology practices because of conversion costs, loss of productivity, and billing problems. Clinical documentation must meet the specificity required by ICD-10 codes or risk denial of payments, which are projected to dramatically increase. In preparation for the now delayed conversion, the ICD-10 transition team at the Seattle Cancer Care Alliance (SCCA) examined the ICD-10 codes for primary hematology/oncology diagnoses and comorbidities of cancer and therapy seen at our institution to identify the need for and feasibility of developing a printable job aid to guide clinical documentation. We found that the variable complexity of ICD-10 codes in hematology/oncology frequently requires nonintuitive specificity likely to be overlooked without prompting. We were able to develop a succinct and facile documentation aid usable in both electronic and printed forms that includes all hematology/oncology diagnoses and the comorbidities most frequently seen in our multidisciplinary institution. This document is organized in a notebook format for easy review and will be continuously improved with feedback from practitioners. It is available for free download from the SCCA Web site.
Assuntos
Codificação Clínica/métodos , Hematologia/organização & administração , Classificação Internacional de Doenças , Oncologia/organização & administração , Neoplasias/classificação , Neoplasias/diagnóstico , Codificação Clínica/normas , Comorbidade , Documentação , Registros Eletrônicos de Saúde , Humanos , Neoplasias/terapia , Estados UnidosRESUMO
PURPOSE: Multidisciplinary tumor boards (MTBs) support high-quality cancer care. Little is known about the impact of information technology (IT) tools on the operational and technical aspects of MTBs. The National Comprehensive Cancer Network EHR Oncology Advisory Group formed a workgroup to investigate the impact of IT tools such as EHRs and virtual conferencing on MTBs. METHODS: The workgroup created a cross-sectional survey for oncology clinicians (eg, pathology, medical, surgical, radiation, etc) participating in MTBs at 31 National Comprehensive Cancer Network member institutions. A standard invitation e-mail was shared with each EHR Advisory Group Member with a hyperlink to the survey, and each member distributed the survey to MTB participants at their institution or identified the appropriate person at their institution to do so. The survey was open from February 26, 2022, to April 26, 2022. Descriptive statistics were applied in the analysis of responses, and a qualitative thematic analysis of open-ended responses was completed. RESULTS: Individuals from 27 institutions participated. Almost all respondents (99%, n = 764 of 767) indicated that their MTBs had participants attending virtually. Most indicated increased attendance (69%, n = 514 of 741) after virtualization with the same or improved quality of discussion (75%, n = 557 of 741) compared with in-person MTBs. Several gaps between the current and ideal state emerged regarding EHR integration: 57% (n = 433 of 758) of respondents noted the importance of adding patients for MTB presentation via the EHR, but only 40% (n = 302 of 747) reported being able to do so most of the time. Similarly, 87% (n = 661 of 760) indicated the importance of documenting recommendations in the EHR, but only 53% (n = 394 of 746) reported this occurring routinely. CONCLUSION: Major gaps include the lack of EHR integration for MTBs. Clinical workflows and EHR functionalities could be improved to further optimize EHRs for MTB management and documentation.
Assuntos
Tecnologia da Informação , Neoplasias , Humanos , Estudos Transversais , Neoplasias/diagnóstico , Neoplasias/epidemiologia , Neoplasias/terapia , Inquéritos e Questionários , OncologiaRESUMO
The strength of the streptavidin/biotin interaction poses challenges for the recovery of biotinylated molecules from streptavidin resins. As an alternative to high-temperature elution in urea-containing buffers, we show that mono-biotinylated proteins can be released with relatively gentle heating in the presence of biotin and 2% SDS/Rapigest, avoiding protein carbamylation and minimizing streptavidin dissociation. We demonstrate the utility of this mild elution strategy in two studies of the human androgen receptor (AR). In the first, in which formaldehyde cross-linked complexes are analyzed in yeast, a mass spectrometry-based comparison of the AR complex using SILAC reveals an association between the androgen-activated AR and the Hsp90 chaperonin, while Hsp70 chaperonins associate specifically with the unliganded complex. In the second study, the endogenous AR is quantified in the LNCaP cell line by absolute SILAC and MRM-MS showing approximately 127,000 AR copies per cell, substantially more than previously measured using radioligand binding.
Assuntos
Biotina/isolamento & purificação , Cromatografia de Afinidade/métodos , Receptores Androgênicos/isolamento & purificação , Estreptavidina/química , Sequência de Aminoácidos , Biotina/metabolismo , Biotinilação , Linhagem Celular Tumoral , Humanos , Espectrometria de Massas/normas , Dados de Sequência Molecular , Fragmentos de Peptídeos/química , Ligação Proteica , Mapeamento de Interação de Proteínas/métodos , Proteômica , Receptores Androgênicos/biossíntese , Receptores Androgênicos/metabolismo , Proteínas Recombinantes de Fusão/biossíntese , Proteínas Recombinantes de Fusão/isolamento & purificação , Proteínas Recombinantes de Fusão/metabolismo , Padrões de Referência , Saccharomyces cerevisiaeRESUMO
Expression of isotopically labeled peptide standards as artificial concatamers (QconCATs) allows for the multiplex quantification of proteins in unlabeled samples by mass spectrometry. We have developed a generalizable QconCAT design strategy, which we term IQcat, wherein concatenated peptides are binned by pI to facilitate MS-sample enrichment by isoelectric focusing. Our method utilizes a rapid (â¼2 weeks), inexpensive and scalable purification of arg/lys labeled IQcat standards in the Escherichia coli auxotroph AT713. With this pipeline, we assess the fidelity of IQcat-based absolute quantification for ten yeast proteins over a broad concentration range in a single information-rich isoelectric fraction. The technique is further employed for a quantitative study of androgen-dependent protein expression in cultured prostate cancer cells.
Assuntos
Focalização Isoelétrica/métodos , Espectrometria de Massas/métodos , Peptídeos/análise , Proteínas/análise , Proteômica/métodos , Sequência de Aminoácidos , Animais , Linhagem Celular Tumoral , Humanos , Focalização Isoelétrica/economia , Masculino , Espectrometria de Massas/economia , Dados de Sequência Molecular , Neoplasias da Próstata/química , Proteômica/economia , Saccharomyces cerevisiae/química , Proteínas de Saccharomyces cerevisiae/análiseRESUMO
In an attempt to identify prostate cancer biomarkers with greater diagnostic and prognostic capabilities, we have developed an integrative proteomic discovery workflow focused on N-linked glycoproteins that refines the target selection process. In this work, hydrazide-based chemistry was used to identify N-linked glycopeptides from 22Rv1 prostate cancer cells cultured in vitro, which were compared with glycopeptides identified from explanted 22Rv1 murine tumor xenografts. One hundred and four human glycoproteins were identified in the former analysis and 75 in the latter, with 40 proteins overlapping between data sets. Of the 40 overlapping proteins, 80% have multiple literature references to the neoplastic process and â¼40% to prostatic neoplasms. These include a number of well-known prostate cancer-associated biomarkers, such as prostate-specific membrane antigen (PSMA). By integrating gene expression data and available literature, we identified members of the overlap data set that deserve consideration as potential prostate cancer biomarkers. Specifically, the identification of the extracellular domain of protein tyrosine phosphatase receptor type F (PTPRF) was of particular interest due to the direct involvement of PTPRF in the control of ß-catenin signaling, as well as dramatically elevated gene expression levels in the prostate compared to other tissues. In this investigation, we demonstrate that the PTPRF E-subunit is more abundant in human prostate tumor tissue compared to normal control and also detectable in murine plasma by immunoblot and ELISA. Specifically, PTPRF distinguishes between animals xenografted with the 22Rv1 cells and control animals as early as 14 days after implantation. This result suggests that the ectodomain of PTPRF has the potential to function as a novel plasma or tissue-based biomarker for prostate cancer. The workflow described adds to the literature of potential biomarker candidates for prostate cancer and demonstrates a pathway to developing new diagnostic assays.
Assuntos
Regulação Neoplásica da Expressão Gênica , Glicoproteínas/análise , Neoplasias da Próstata/diagnóstico , Proteômica/métodos , Proteínas Tirosina Fosfatases Classe 2 Semelhantes a Receptores/metabolismo , Animais , Biomarcadores Tumorais/sangue , Biomarcadores Tumorais/metabolismo , Western Blotting , Ensaio de Imunoadsorção Enzimática , Glicoproteínas/genética , Glicoproteínas/metabolismo , Glicosilação , Humanos , Masculino , Camundongos , Camundongos Endogâmicos NOD , Camundongos SCID , Neoplasias da Próstata/genética , Neoplasias da Próstata/metabolismo , Estrutura Terciária de Proteína , Proteínas Tirosina Fosfatases Classe 2 Semelhantes a Receptores/sangue , Proteínas Tirosina Fosfatases Classe 2 Semelhantes a Receptores/genética , Fatores de Tempo , Ensaios Antitumorais Modelo de Xenoenxerto , beta Catenina/genética , beta Catenina/metabolismoRESUMO
PURPOSE: Clinical notes function as the de facto handoff between providers and assume great importance during unplanned medical encounters. An organized and thorough oncology history is essential in care coordination. We sought to understand reader preferences for oncology history organization by comparing between chronologic and narrative formats. METHODS: A convenience sample of 562 clinicians from 19 National Comprehensive Cancer Network Member Institutions responded to a survey comparing two formats of oncology histories, narrative and chronologic, for the same patient. Both histories were consensus-derived real-world examples. Each history was evaluated using semantic differential attributes (thorough, useful, organized, comprehensible, and succinct). Respondents choose a preference between the two styles for history gathering and as the basis of a new note. Open-ended responses were also solicited. RESULTS: Respondents preferred the chronologic over the narrative history to prepare for a visit with an unknown patient (66% preference) and as a basis for their own note preparation (77% preference) (P < .01). The chronologic summary was preferred in four of the five measured attributes (useful, organized, comprehensible, and succinct); the narrative summary was favored for thoroughness (P < .01). Open-ended responses reflected the attribute scoring and noted the utility of content describing social determinants of health in the narrative history. CONCLUSION: Respondents of this convenience sample preferred a chronologic oncology history to a concise narrative history. Further studies are needed to determine the optimal structure and content of chronologic documentation for oncology patients and the provider effort to use this format.
Assuntos
Documentação , Neoplasias , Humanos , Inquéritos e QuestionáriosRESUMO
Multiple reaction monitoring (MRM) is a highly sensitive and increasingly popular method of targeted mass spectrometry (MS) that can be used to selectively detect and quantify peptides and their corresponding proteins of interest within biological samples. The sensitivity of MRM-MS is highly dependent upon the tuning of transition-specific parameters, especially the collision energy (CE) applied during peptide fragmentation. Currently, empirical equations for CE work best for y-type ions and are much less effective for other types of transitions, such as b-type ions and small y-type transitions across particular amide bonds, which could also be useful for MRM-MS if optimized for maximum signal transmission. In this work, we have performed a CE optimization of all transitions for 80 doubly charged peptides, the results of which were used to define separate CE equations for b-ions and y-ions, as well as for small y-type ions derived from the fragmentation of amide bonds bounded on the amino-terminal side by aspartic or glutamic acid residues (D/E-X transitions). This analysis yielded four major observations: (1) b-ions tend to require lower collision energies than y-ions for optimal fragmentation, while D/E-X transitions tend to require more; (2) CE equations predict the optimal CEs more closely when product ion m/z dependence is included, in addition to the current standard of precursor ion m/z dependence; (3) separate CE equations for y-ions, b-ions, and D/E-X transitions are more effective than the previous one-size-fits-all equations, but best results are achieved by optimizing transitions individually; and (4) while b-ions gain substantial signal from CE optimization-often increases of several-fold-they still tend to rank lower than y-ions from the same peptide. These results confirm the notion that y-ions are usually the first-choice transitions for MRM experiments but also demonstrate, for the first time, that b-ions can be viable targets as well, if the proper collision energies are used.
Assuntos
Espectrometria de Massas/métodos , Fragmentos de Peptídeos/química , Proteínas/química , Proteômica/métodos , Biologia Computacional , Modelos Lineares , Fragmentos de Peptídeos/metabolismo , Proteínas/metabolismo , Sensibilidade e Especificidade , Tripsina/metabolismoRESUMO
Mass spectrometry-based proteomics is a maturing discipline of biologic research that is experiencing substantial growth. Instrumentation has steadily improved over time with the advent of faster and more sensitive instruments collecting ever larger data files. Consequently, the computational process of matching a peptide fragmentation pattern to its sequence, traditionally accomplished by sequence database searching and more recently also by spectral library searching, has become a bottleneck in many mass spectrometry experiments. In both of these methods, the main rate-limiting step is the comparison of an acquired spectrum with all potential matches from a spectral library or sequence database. This is a highly parallelizable process because the core computational element can be represented as a simple but arithmetically intense multiplication of two vectors. In this paper, we present a proof of concept project taking advantage of the massively parallel computing available on graphics processing units (GPUs) to distribute and accelerate the process of spectral assignment using spectral library searching. This program, which we have named FastPaSS (for Fast Parallelized Spectral Searching), is implemented in CUDA (Compute Unified Device Architecture) from NVIDIA, which allows direct access to the processors in an NVIDIA GPU. Our efforts demonstrate the feasibility of GPU computing for spectral assignment, through implementation of the validated spectral searching algorithm SpectraST in the CUDA environment.
Assuntos
Biologia Computacional/métodos , Computadores , Interpretação Estatística de Dados , Proteômica/métodos , Software , Espectrometria de Massas em Tandem/métodos , Algoritmos , Modelos Moleculares , Peso Molecular , Proteômica/instrumentaçãoRESUMO
The methylotrophic yeast Pichia pastoris is a powerful eukaryotic platform for the production of heterologous protein. Recent publication of the P. pastoris genome has facilitated strain development toward biopharmaceutical and environmental science applications and has advanced the organism as a model system for the study of peroxisome biogenesis and methanol metabolism. Here we report the development of a P. pastoris arg-/lys- auxotrophic strain compatible with SILAC (stable isotope labeling by amino acids in cell culture) proteomic studies, which is capable of generating large quantities of isotopically labeled protein for mass spectrometry-based biomarker measurements. We demonstrate the utility of this strain to produce high purity human serum albumin uniformly labeled with isotopically heavy arginine and lysine. In addition, we demonstrate the first quantitative proteomic analysis of methanol metabolism in P. pastoris, reporting new evidence for a malate-aspartate NADH shuttle mechanism in the organism. This strain will be a useful model organism for the study of metabolism and peroxisome generation.
Assuntos
Marcação por Isótopo , Pichia/genética , Albumina Sérica/biossíntese , Sequência de Aminoácidos , Proteínas Fúngicas/genética , Proteínas Fúngicas/metabolismo , Técnicas de Inativação de Genes , Vetores Genéticos , Humanos , Metanol/metabolismo , Dados de Sequência Molecular , Peroxissomos/metabolismo , Pichia/enzimologia , Pichia/metabolismo , Proteômica , Proteínas Recombinantes/biossíntese , Proteínas Recombinantes/metabolismo , Proteínas Recombinantes/normas , Padrões de Referência , Vesículas Secretórias/metabolismo , Albumina Sérica/metabolismo , Albumina Sérica/normas , Espectrometria de Massas em Tandem/normas , Regulação para CimaRESUMO
Improved approaches for the detection of common epithelial malignancies are urgently needed to reduce the worldwide morbidity and mortality caused by cancer. MicroRNAs (miRNAs) are small ( approximately 22 nt) regulatory RNAs that are frequently dysregulated in cancer and have shown promise as tissue-based markers for cancer classification and prognostication. We show here that miRNAs are present in human plasma in a remarkably stable form that is protected from endogenous RNase activity. miRNAs originating from human prostate cancer xenografts enter the circulation, are readily measured in plasma, and can robustly distinguish xenografted mice from controls. This concept extends to cancer in humans, where serum levels of miR-141 (a miRNA expressed in prostate cancer) can distinguish patients with prostate cancer from healthy controls. Our results establish the measurement of tumor-derived miRNAs in serum or plasma as an important approach for the blood-based detection of human cancer.
Assuntos
Biomarcadores Tumorais/genética , Regulação Neoplásica da Expressão Gênica , MicroRNAs/sangue , MicroRNAs/genética , Animais , Clonagem Molecular , Perfilação da Expressão Gênica , Humanos , Masculino , Camundongos , Transplante de Neoplasias , Neoplasias/metabolismo , Neoplasias da Próstata/sangue , Neoplasias da Próstata/genética , RNA Neoplásico/sangue , RNA Neoplásico/metabolismo , Ribonucleases/metabolismo , Sensibilidade e EspecificidadeRESUMO
PURPOSE: The use of telemedicine expanded dramatically in March 2020 following the COVID-19 pandemic. We sought to assess oncologist perspectives on telemedicine's present and future roles (both phone and video) for patients with cancer. METHODS: The National Comprehensive Cancer Network (NCCN) Electronic Health Record (EHR) Oncology Advisory Group formed a Workgroup to assess the state of oncology telemedicine and created a 20-question survey. NCCN EHR Oncology Advisory Group members e-mailed the survey to providers (surgical, hematology, gynecologic, medical, and radiation oncology physicians and clinicians) at their home institution. RESULTS: Providers (N = 1,038) from 26 institutions responded in Summer 2020. Telemedicine (phone and video) was compared with in-person visits across clinical scenarios (n = 766). For reviewing benign follow-up data, 88% reported video and 80% reported telephone were the same as or better than office visits. For establishing a personal connection with patients, 24% and 7% indicated video and telephone, respectively, were the same as or better than office visits. Ninety-three percent reported adverse outcomes attributable to telemedicine visits never or rarely occurred, whereas 6% indicated they occasionally occurred (n = 801). Respondents (n = 796) estimated 46% of postpandemic visits could be virtual, but challenges included (1) lack of patient access to technology, (2) inadequate clinical workflows to support telemedicine, and (3) insurance coverage uncertainty postpandemic. CONCLUSION: Telemedicine appears effective across a variety of clinical scenarios. Based on provider assessment, a substantial fraction of visits for patients with cancer could be effectively and safely conducted using telemedicine. These findings should influence regulatory and infrastructural decisions regarding telemedicine postpandemic for patients with cancer.
Assuntos
COVID-19 , Neoplasias , Oncologistas , Telemedicina , Feminino , Humanos , Neoplasias/terapia , Pandemias , SARS-CoV-2 , Inquéritos e QuestionáriosRESUMO
Autologous hematopoietic cell transplantation (AHCT) is a standard of care for several subtypes of high-risk lymphoma, but durable remissions are not achieved in the majority of patients. Intensified conditioning using CD45-targeted antibody-radionuclide conjugate (ARC) preceding AHCT may improve outcomes in lymphoma by permitting the delivery of curative doses of radiation to disease sites while minimizing toxicity. We performed sequential phase I trials of escalating doses of yttrium-90 (90Y)-labeled anti-CD45 antibody with or without BEAM (carmustine, etoposide, cytarabine, melphalan) chemotherapy followed by AHCT in adults with relapsed/refractory or high-risk B cell non-Hodgkin lymphoma (NHL), T cell NHL (T-NHL), or Hodgkin lymphoma (HL). Twenty-one patients were enrolled (16 NHL, 4 HL, 1 T-NHL). Nineteen patients received BEAM concurrently. No dose-limiting toxicities were observed; therefore, the maximum tolerated dose is estimated to be ≥34 Gy to the liver. Nonhematologic toxicities and engraftment kinetics were similar to standard myeloablative AHCT. Late myeloid malignancies and 100-day nonrelapse deaths were not observed. At a median follow-up of 5 years, the estimates of progression-free and overall survival of 19 patients were 37% and 68%, respectively. Two patients did not receive BEAM; one had stable disease and the other progressive disease post-transplant. The combination of 90Y-anti-CD45 with BEAM and AHCT was feasible and tolerable in patients with relapsed and refractory lymphoma. The use of anti-CD45 ARC as an adjunct to hematopoietic cell transplantation regimens or in combination with novel therapies/immunotherapies should be further explored based on these and other data.
Assuntos
Transplante de Células-Tronco Hematopoéticas , Linfoma , Adulto , Protocolos de Quimioterapia Combinada Antineoplásica/uso terapêutico , Humanos , Imunoterapia , Linfoma/terapia , Recidiva Local de Neoplasia/terapia , Radioisótopos de ÍtrioRESUMO
The Trans-Proteomic Pipeline (TPP) is a suite of software tools for the analysis of MS/MS data sets. The tools encompass most of the steps in a proteomic data analysis workflow in a single, integrated software system. Specifically, the TPP supports all steps from spectrometer output file conversion to protein-level statistical validation, including quantification by stable isotope ratios. We describe here the full workflow of the TPP and the tools therein, along with an example on a sample data set, demonstrating that the setup and use of the tools are straightforward and well supported and do not require specialized informatic resources or knowledge.
Assuntos
Bases de Dados de Proteínas , Proteômica/métodos , Software , Biologia Computacional , Armazenamento e Recuperação da Informação , Marcação por Isótopo , Análise de Sequência de Proteína , Espectrometria de Massas em TandemRESUMO
Mass spectrometry-based proteomics is typically performed using high performance liquid chromatography (HPLC) to introduce peptides into the instrument via electrospray ionization. A variety of configurations exist with varying degrees of precision and cost, but the ultimate goal is the reproducible delivery of peptides in well-separated elution peaks. It is well-known that the quality of chromatography can have a dramatic effect on sample identification as well as run-to-run reproducibility, which is especially important for quantitative analyses. Despite the importance of the HPLC system for both shotgun and targeted proteomics, there are few tools available to monitor HPLC performance. In this paper, we describe a new open-source software application, named ChromEval, to allow rapid assessment of HPLC performance, as well as to provide other metrics of mass spectrometer performance, including mass accuracy calibration. ChromEval permits the user to visually monitor the elution of a set of standard peptides in quality control runs interspersed among a regular workflow. To perform these tasks, ChromEval searches mzXML files using Tandem and presents the peptide results in a graphical user interface (GUI) that allows fast assessment of chromatography by visualization of superimposed elution peaks. This tool facilitates the identification and troubleshooting of chromatography problems such as retention time shifts and variance in sample loading due to autosampler error. It also provides crude but consistent metrics of instrument performance including mass accuracy calibration and number of peptides identified from the standard mixture. ChromEval generates easily interpretable data quickly and thereby enables go/no-go decision making during intensive instrument operation.
Assuntos
Cromatografia Líquida de Alta Pressão/métodos , Proteínas/análise , Proteômica/métodos , Software , Cromatografia Líquida de Alta Pressão/economia , Peptídeos/análise , Proteômica/economia , Fatores de TempoRESUMO
Multiple reaction monitoring (MRM) mass spectrometry identifies and quantifies specific peptides in a complex mixture with very high sensitivity and speed and thus has promise for the high throughput screening of clinical samples for candidate biomarkers. We have developed an interactive software platform, called MRMer, for managing highly complex MRM-MS experiments, including quantitative analyses using heavy/light isotopic peptide pairs. MRMer parses and extracts information from MS files encoded in the platform-independent mzXML data format. It extracts and infers precursor-product ion transition pairings, computes integrated ion intensities, and permits rapid visual curation for analyses exceeding 1000 precursor-product pairs. Results can be easily output for quantitative comparison of consecutive runs. Additionally MRMer incorporates features that permit the quantitative analysis experiments including heavy and light isotopic peptide pairs. MRMer is open source and provided under the Apache 2.0 license.
Assuntos
Espectrometria de Massas/métodos , Espectrometria de Massas/estatística & dados numéricos , Proteômica/métodos , Proteômica/estatística & dados numéricos , Software , Fragmentos de Peptídeos/isolamento & purificação , Fosfopiruvato Hidratase/isolamento & purificação , Fosfopiruvato Hidratase/metabolismo , Saccharomyces cerevisiae/enzimologia , Saccharomyces cerevisiae/genética , Proteínas de Saccharomyces cerevisiae/isolamento & purificação , Proteínas de Saccharomyces cerevisiae/metabolismo , TripsinaRESUMO
Multiple reaction monitoring mass spectrometry (MRM-MS) is a targeted analysis method that has been increasingly viewed as an avenue to explore proteomes with unprecedented sensitivity and throughput. We have developed a software tool, called MaRiMba, to automate the creation of explicitly defined MRM transition lists required to program triple quadrupole mass spectrometers in such analyses. MaRiMba creates MRM transition lists from downloaded or custom-built spectral libraries, restricts output to specified proteins or peptides, and filters based on precursor peptide and product ion properties. MaRiMba can also create MRM lists containing corresponding transitions for isotopically heavy peptides, for which the precursor and product ions are adjusted according to user specifications. This open-source application is operated through a graphical user interface incorporated into the Trans-Proteomic Pipeline, and it outputs the final MRM list to a text file for upload to MS instruments. To illustrate the use of MaRiMba, we used the tool to design and execute an MRM-MS experiment in which we targeted the proteins of a well-defined and previously published standard mixture.
Assuntos
Bases de Dados de Proteínas , Espectrometria de Massas/métodos , Proteômica/métodos , Interface Usuário-Computador , Animais , Pulmão/química , Masculino , Camundongos , Camundongos Endogâmicos BALB C , Peptídeos/química , Proteínas/química , Reprodutibilidade dos Testes , Biologia de SistemasRESUMO
Immonium ions have been largely overlooked during the rapid expansion of mass spectrometry-based proteomics largely due to the dominance of ion trap instruments in the field. However, immonium ions are visible in hybrid quadrupole-time-of-flight (QTOF) mass spectrometers, which are now widely available. We have created the largest database to date of high-confidence sequence assignments to characterize the appearance of immonium ions in CID spectra using a QTOF instrument under "typical" operating conditions. With these data, we are able to demonstrate excellent correlation between immonium ion peak intensity and the likelihood of the appearance of the expected amino acid in the assigned sequence for phenylalanine, tyrosine, tryptophan, proline, histidine, valine, and the indistinguishable leucine and isoleucine residues. In addition, we have clearly demonstrated a positional effect whereby the proximity of the amino acid generating the immonium ion to the amino terminal of the peptide correlates with the strength of the immonium ion peak. This compositional information provided by the immonium ion peaks could substantially improve algorithms used for spectral assignment in mass spectrometry analysis using QTOF platforms.
Assuntos
Biologia Computacional , Espectrometria de Massas/métodos , Compostos de Amônio Quaternário/química , Sequência de Aminoácidos , Bases de Dados de Proteínas , Íons/química , Dados de Sequência Molecular , Concentração Osmolar , Peptídeos/análise , Peptídeos/química , Saccharomyces cerevisiae , Fatores de TempoRESUMO
Quantitative proteome profiling using stable isotope protein tagging and automated tandem mass spectrometry (MS/MS) is an emerging technology with great potential for the functional analysis of biological systems and for the detection of clinical diagnostic or prognostic marker proteins. Owing to the enormous complexity of proteomes, their comprehensive analysis is an as-yet-unresolved technical challenge. However, biologically or clinically important information can be obtained if specific, information-rich protein classes, or sub-proteomes, are isolated and analyzed. Glycosylation is the most common post-translational modification. Here we describe a method for the selective isolation, identification and quantification of peptides that contain N-linked carbohydrates. It is based on the conjugation of glycoproteins to a solid support using hydrazide chemistry, stable isotope labeling of glycopeptides and the specific release of formerly N-linked glycosylated peptides via peptide- N-glycosidase F (PNGase F). The recovered peptides are then identified and quantified by MS/MS. We applied the approach to the analysis of plasma membrane proteins and proteins contained in human blood serum.