A targeted proteomics–based pipeline for verification of biomarkers in plasma

Whiteaker, Jeffrey R.; Lin, Chenwei; Kennedy, Jacob J.; Hou, Liming; Trute, Mary; Sokal, Izabela; Yan, Ping; Schoenherr, Regine M.; Zhao, Lei; Voytovich, Uliana J.; Kelly-Spratt, Karen S.; Krasnoselsky, Alexei L.; Gafken, Philip R.; Hogan, Jason M.; Jones, Lisa; Wang, Pei; Amon, Lynn M.; Chodosh, Lewis A.; Nelson, Peter S.; McIntosh, Martin W.; Kemp, Christopher J.; Paulovich, Amanda G.

doi:10.1038/nbt.1900

Cited by 329 publications

(336 citation statements)

References 42 publications

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“…SRM, primarily per-formed on triple quadrupole (QqQ) MS, has emerged as the MS "gold-standard" for targeted proteomics (21) and is a broadly accepted alternative to the traditional multiplexed immunoassay (20). Numerous studies have successfully employed QqQ SRM for both absolute and relative quantitation of analytes in applications ranging from clinical diagnostics (22)(23)(24)(25)(26)(27) to whole systems analyses (28 -30). The rising popularity and promise of the SRM technique have also spawned a plethora of new analysis approaches and software tools.…”

mentioning

confidence: 99%

Parallel Reaction Monitoring for High Resolution and High Mass Accuracy Quantitative, Targeted Proteomics

Peterson

Russell

Bailey

et al. 2012

Molecular & Cellular Proteomics

1,044

939

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Selected reaction monitoring on a triple quadrupole mass spectrometer is currently experiencing a renaissance within the proteomics community for its, as yet, unparalleled ability to characterize and quantify a set of proteins reproducibly, completely, and with high sensitivity. Given the immense benefit that high resolution and accurate mass instruments have brought to the discovery proteomics field, we wondered if highly accurate mass measurement capabilities could be leveraged to provide benefits in the targeted proteomics domain as well. Here, we propose a new targeted proteomics paradigm centered on the use of next generation, quadrupole-equipped high resolution and accurate mass instruments: parallel reaction monitoring (PRM). In PRM, the third quadrupole of a triple quadrupole is substituted with a high resolution and accurate mass mass analyzer to permit the parallel detection of all target product ions in one, concerted high resolution mass analysis. We detail the analytical performance of the PRM method, using a quadrupoleequipped bench-top Orbitrap MS, and draw a performance comparison to selected reaction monitoring in terms of run-to-run reproducibility, dynamic range, and measurement accuracy. In addition to requiring minimal upfront method development and facilitating automated data analysis, PRM yielded quantitative data over a wider dynamic range than selected reaction monitoring in the presence of a yeast background matrix because of PRM's high selectivity in the mass-to-charge domain. With achievable linearity over the quantifiable dynamic range found to be statistically equal between the two methods, our investigation suggests that PRM will be a promising new addition to the quantitative proteomics toolbox. Molecular & Cellular Proteomics 11: 10.1074/ mcp.O112.020131, 1475-1488, 2012.The most widespread protein sequencing technique is the shotgun method. Proteins are digested into peptides, chromatographically separated, and measured by mass spectrometers (1-10). Many types of mass spectrometers are used-quadrupole ion traps, quadrupole ion trap hybrids such as the QLT (quadrupole linear ion trap)-Orbitrap or QLT-FT-ICR, and quadrupole time-of-flight (Q-TOF) hybrids-but, the experiments, from the MS measurement onward, are basically identical: the masses of eluting cationic peptide precursors are measured in a MS scan, and the most abundant precursors are selected in series for successive tandem MS events (MS/MS). This process, called data-dependent acquisition, continues for the duration of a chromatographic separation, and constant MS operation in this manner can generate hundreds of thousands of spectra in days. These spectra are then mapped to peptide or protein sequence databases using highly-evolved database search algorithms (11-13). Successful results can be obtained within just a few days and are nothing short of spectacular: tens of thousands of unique peptide spectral matches mapping to several thousand unique protein isoforms have become the norm. Although this approach certainly ...

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confidence: 99%

Parallel Reaction Monitoring for High Resolution and High Mass Accuracy Quantitative, Targeted Proteomics

Peterson

Russell

Bailey

et al. 2012

Molecular & Cellular Proteomics

1,044

939

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“…However, despite numerous biomarker publications over the years (1), only a handful of new cancer biomarkers have successfully completed the journey from discovery, qualification, to verification and validation (2)(3)(4). One possible way to overcome this challenge is to develop an integrated biomarker pipeline that facilitates the smooth and successful transition from discovery to validation (5)(6)(7)(8)(9)(10). The first and foremost consideration in an integrated pipeline is the sample source.…”

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confidence: 99%

Serum Glycoprotein Biomarker Discovery and Qualification Pipeline Reveals Novel Diagnostic Biomarker Candidates for Esophageal Adenocarcinoma

Shah

Cao

Choi

et al. 2015

Molecular & Cellular Proteomics

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We report an integrated pipeline for efficient serum glycoprotein biomarker candidate discovery and qualification that may be used to facilitate cancer diagnosis and management. The discovery phase used semi-automated lectin magnetic bead array (LeMBA)-coupled tandem mass spectrometry with a dedicated data-housing and analysis pipeline; GlycoSelector (http://glycoselector.di. uq.edu.au). The qualification phase used lectin magnetic bead array-multiple reaction monitoring-mass spectrometry incorporating an interactive web-interface, Shiny mixOmics (http://mixomics-projects.di.uq.edu.au/Shiny), for univariate and multivariate statistical analysis. Relative quantitation was performed by referencing to a spiked-in glycoprotein, chicken ovalbumin. We applied this workflow to identify diagnostic biomarkers for esophageal adenocarcinoma (EAC), a life threatening malignancy with poor prognosis in the advanced setting. EAC develops from metaplastic condition Barrett's esophagus (BE). Currently diagnosis and monitoring of at-risk patients is through endoscopy and biopsy, which is expensive and requires hospital admission. Hence there is a clinical need for a noninvasive diagnostic biomarker of EAC. In total 89 patient samples from healthy controls, and patients with BE or EAC were screened in discovery and qualification stages. Of the 246 glycoforms measured in the qualification stage, 40 glycoforms (as measured by lectin affinity) qualified as candidate serum markers. The top candidate for distinguishing healthy from BE patients' group was Narcissus pseudonarcissus lectin (

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“…In 2011 a complete verification pipeline of biomarker candidates in plasma was presented in a tour‐de‐force study by Whiteaker and coworkers 129. They integrated 13 datasets from discovery proteomics and genomics to arrive at >1000 candidate proteins in a mouse model of breast cancer and used data‐dependent prioritization to triage candidates, developing assays for 88 proteins evaluated across 80 plasma samples, finding 36 over‐expressed proteins with excellent analytical performance.…”

Section: Clinical Applicationsmentioning

confidence: 99%

Applications of targeted proteomics in systems biology and translational medicine

et al. 2015

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Biological systems are composed of numerous components of which proteins are of particularly high functional significance. Network models are useful abstractions for studying these components in context. Network representations display molecules as nodes and their interactions as edges. Because they are difficult to directly measure, functional edges are frequently inferred from suitably structured datasets consisting of the accurate and consistent quantification of network nodes under a multitude of perturbed conditions. For the precise quantification of a finite list of proteins across a wide range of samples, targeted proteomics exemplified by selected/multiple reaction monitoring (SRM, MRM) mass spectrometry has proven useful and has been applied to a variety of questions in systems biology and clinical studies. Here, we survey the literature of studies using SRM‐MS in systems biology and clinical proteomics. Systems biology studies frequently examine fundamental questions in network biology, whereas clinical studies frequently focus on biomarker discovery and validation in a variety of diseases including cardiovascular disease and cancer. Targeted proteomics promises to advance our understanding of biological networks and the phenotypic significance of specific network states and to advance biomarkers into clinical use.

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A targeted proteomics–based pipeline for verification of biomarkers in plasma

Cited by 329 publications

References 42 publications

Parallel Reaction Monitoring for High Resolution and High Mass Accuracy Quantitative, Targeted Proteomics

Parallel Reaction Monitoring for High Resolution and High Mass Accuracy Quantitative, Targeted Proteomics

Serum Glycoprotein Biomarker Discovery and Qualification Pipeline Reveals Novel Diagnostic Biomarker Candidates for Esophageal Adenocarcinoma

Applications of targeted proteomics in systems biology and translational medicine

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