Demonstrating the feasibility of large-scale development of standardized assays to quantify human proteins

Kennedy, Jacob J.; Abbatiello, Susan E.; Kim, Kyunggon; Yan, Ping; Whiteaker, Jeffrey R.; Lin, Chenwei; Kim, Jun Seok; Zhang, Yuzheng; Wang, Xianlong; Ivey, Richard G.; Zhao, Lei; Min, Hophil; Lee, Young-Ju; Yu, Myeong Hee; Yang, Eun Gyeong; Lee, Cheolju; Wang, Pei; Rodriguez, Henry; Kim, Youngsoo; Carr, Steven A.; Paulovich, Amanda G.

doi:10.1038/nmeth.2763

Cited by 176 publications

(198 citation statements)

References 59 publications

Supporting

Mentioning

194

Contrasting

Order By: Relevance

“…For the reproducible and accurate quantification of tryptic peptides in complex proteome digests, the S/MRM technique has been shown to reach a high dynamic range of about five orders of magnitude, as well as excellent interlaboratory reproducibility, with a median coefficient of variation (CV) of ϳ5% (99). Similar analytical performances were also observed using the PRM approach (100 -102).…”

Section: Identification and Quantification Of Mhc-associated Peptidesmentioning

confidence: 77%

Analysis of Major Histocompatibility Complex (MHC) Immunopeptidomes Using Mass Spectrometry*

Caron

Kowalewski

Koh

et al. 2015

Molecular & Cellular Proteomics

198

118

View full text Add to dashboard Cite

The myriad of peptides presented at the cell surface by class I and class II major histocompatibility complex (MHC) molecules are referred to as the immunopeptidome and are of great importance for basic and translational science. For basic science, the immunopeptidome is a critical component for understanding the immune system; for translational science, exact knowledge of the immunopeptidome can directly fuel and guide the development of next-generation vaccines and immunotherapies against autoimmunity, infectious diseases, and cancers. In this mini-review, we summarize established isolation techniques as well as emerging mass spectrometry-based platforms (i.e. SWATH-MS) to identify and quantify MHC-associated peptides. We also highlight selected biological applications and discuss important current technical limitations that need to be solved to accelerate the development of this field. Molecular & Cellular

show abstract

Section: Identification and Quantification Of Mhc-associated Peptidesmentioning

confidence: 77%

Analysis of Major Histocompatibility Complex (MHC) Immunopeptidomes Using Mass Spectrometry*

Caron

Kowalewski

Koh

et al. 2015

Molecular & Cellular Proteomics

198

118

View full text Add to dashboard Cite

show abstract

“…The bulk of recent work has focused on candidate discovery and overcoming the associated challenges related to tissues and bodily fluids. Targeted proteomics can be used to validate biomarkers found in a project's discovery phase across many patient samples with high accuracy and reproducibility 29, 74. Cima and coworkers successfully applied this strategy by initially using shotgun data to establish a protein list of 44 candidates.…”

Section: Clinical Applicationsmentioning

confidence: 99%

“…Targeted proteomics is best suited to meet these needs. Multiple studies clearly demonstrated the reproducibility of SRM‐MS across laboratories 29, 30. SRM‐MS has been applied to quantify protein levels of liver tissue across 40 strains of BDX mouse 31 and quantitative trait analysis (QTL) of 78 Saccharomyces cerevisiae strains 32.…”

Section: Introductionmentioning

confidence: 99%

Applications of targeted proteomics in systems biology and translational medicine

et al. 2015

View full text Add to dashboard Cite

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.

show abstract

“…High quality and crude isotopically labeled standard peptides with C-terminal 15 N-and 13 C-labeled arginine and lysine residues (HeavyPeptide AQUA TM Ultimate at 5 pmol/l Ϯ 5% and PEPotecs TM ) were synthesized by Thermo Fisher Scientific (Bremen, Germany). C 18 Sep-Pak cartridges (Sep-Pak Vac, 1 ml, 50 mg, tC18) were obtained from Waters (Milford, MA), and all other reagents and chemicals were purchased from Sigma-Aldrich. All buffers were prepared with ultrapure water.…”

Section: Chemicalsmentioning

confidence: 99%

Discovery and Targeted Proteomics on Cutaneous Biopsies Infected by Borrelia to Investigate Lyme Disease*

Schnell

Bœuf

Westermann

et al. 2015

Molecular & Cellular Proteomics

View full text Add to dashboard Cite

Lyme disease is the most important vector-borne disease in the Northern hemisphere and represents a major public health challenge with insufficient means of reliable diagnosis. Skin is rarely investigated in proteomics but constitutes in the case of Lyme disease the key interface where the pathogens can enter, persist, and multiply. Therefore, we investigated proteomics on skin samples to detect Borrelia proteins directly in cutaneous biopsies in a robust and specific way. We first set up a discovery gel prefractionation-LC-MS/MS approach on a murine model infected by Borrelia burgdorferi sensu stricto that allowed the identification of 25 Borrelia proteins among more than 1300 mouse proteins. Then we developed a targeted gel prefractionation-LC-selected reaction monitoring (SRM) assay to detect 9/33 Borrelia proteins/peptides in mouse skin tissue samples using heavy labeled synthetic peptides. We successfully transferred this assay from the mouse model to human skin biopsies (naturally infected by Borrelia), and we were able to detect two Borrelia proteins: OspC and flagellin. Considering the extreme variability of OspC, we developed an extended SRM assay to target a large set of variants. This assay afforded the detection of nine peptides belonging to either OspC or flagellin in human skin biopsies. We further shortened the sample preparation and showed that Borrelia is detectable in mouse and human skin biopsies by directly using a liquid digestion followed by LC-SRM analysis without any prefractionation. This study thus shows that a targeted SRM approach is a promising tool for the early direct diagnosis of Lyme disease with high sensitivity (<10 fmol of OspC/mg of human skin biopsy). Molecular & Cellular Proteomics

show abstract

Demonstrating the feasibility of large-scale development of standardized assays to quantify human proteins

Cited by 176 publications

References 59 publications

Analysis of Major Histocompatibility Complex (MHC) Immunopeptidomes Using Mass Spectrometry*

Analysis of Major Histocompatibility Complex (MHC) Immunopeptidomes Using Mass Spectrometry*

Applications of targeted proteomics in systems biology and translational medicine

Discovery and Targeted Proteomics on Cutaneous Biopsies Infected by Borrelia to Investigate Lyme Disease*

Contact Info

Product

Resources

About