<scp>PASSEL</scp>: The <scp>P</scp>eptide<scp>A</scp>tlas <scp>SRM</scp>experiment library

Farrah, Terry; Deutsch, Eric W.; Kreisberg, Richard; Sun, Zhi; Campbell, D. S.; Mendoza, Luis; Kusebauch, Ulrike; Brusniak, Mi-Youn; Hüttenhain, Ruth; Schiess, Ralph; Selevsek, Nathalie; Aebersold, Ruedi; Moritz, Robert L.

doi:10.1002/pmic.201100515

Cited by 206 publications

(171 citation statements)

References 23 publications

(23 reference statements)

Supporting

Mentioning

171

Contrasting

Order By: Relevance

“…SRM data have been deposited at the PeptideAtlas SRM Experiment Library and are accessible via the http://www.peptideatlas.org/PASS/ PASS00282 (Farrah et al, 2012).…”

Section: Absolute Peptide Quantificationmentioning

confidence: 99%

Functional Characterization of the Small Regulatory Subunit PetP from the Cytochrome b₆f Complex in Thermosynechococcus elongatus

Rexroth

Veit

et al. 2014

Plant Cell

View full text Add to dashboard Cite

The cyanobacterial cytochrome b 6 f complex is central for the coordination of photosynthetic and respiratory electron transport and also for the balance between linear and cyclic electron transport. The development of a purification strategy for a highly active dimeric b 6 f complex from the thermophilic cyanobacterium Thermosynechococcus elongatus BP-1 enabled characterization of the structural and functional role of the small subunit PetP in this complex. Moreover, the efficient transformability of this strain allowed the generation of a DpetP mutant. Analysis on the whole-cell level by growth curves, photosystem II light saturation curves, and P700 + reduction kinetics indicate a strong decrease in the linear electron transport in the mutant strain versus the wild type, while the cyclic electron transport via photosystem I and cytochrome b 6 f is largely unaffected. This reduction in linear electron transport is accompanied by a strongly decreased stability and activity of the isolated DpetP complex in comparison with the dimeric wild-type complex, which binds two PetP subunits. The distinct behavior of linear and cyclic electron transport may suggest the presence of two distinguishable pools of cytochrome b 6 f complexes with different functions that might be correlated with supercomplex formation.

show abstract

“…SRM data have been deposited at the PeptideAtlas SRM Experiment Library and are accessible via the http://www.peptideatlas.org/PASS/ PASS00282 (Farrah et al, 2012).…”

Section: Absolute Peptide Quantificationmentioning

confidence: 99%

Functional Characterization of the Small Regulatory Subunit PetP from the Cytochrome b₆f Complex in Thermosynechococcus elongatus

Rexroth

Veit

et al. 2014

Plant Cell

View full text Add to dashboard Cite

show abstract

“…For example, many algorithms and software tools have been developed to expedite assay development by aiding in the selection of proteotypic peptides (31), peptide transitions, and instrument parameters (reviewed in Cham Mead et al (32)). Additionally, through community effort, several publicly available databases of tandem MS spectra (33)(34)(35)(36)(37)(38)(39) and validated SRM assays (40,41) are available to provide empirical guides to transition selection and assay development. Several groups have also presented elegant solutions to maximize instrument duty cycle and improve assay specificity.…”

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

1,107

953

View full text Add to dashboard Cite

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 ...

show abstract

“…The Human Plasma Proteome Peptide Atlas was launched to provide a knowledge‐base for targeted assays 15, 76. Inspiration for the use of these assays in the clinical setting comes from the small molecule clinical chemistry community where targeted MS is the gold standard for clinical assays quantifying inborn errors of metabolism, drugs and their metabolites, and steroids and biogenic amines 69.…”

Section: Clinical Applicationsmentioning

confidence: 99%

Applications of targeted proteomics in systems biology and translational medicine

et al. 2015

Self Cite

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

PASSEL: The PeptideAtlas SRMexperiment library

Cited by 206 publications

References 23 publications

Functional Characterization of the Small Regulatory Subunit PetP from the Cytochrome b₆f Complex in Thermosynechococcus elongatus

Functional Characterization of the Small Regulatory Subunit PetP from the Cytochrome b₆f Complex in Thermosynechococcus elongatus

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

Applications of targeted proteomics in systems biology and translational medicine

Contact Info

Product

Resources

About

PASSEL: The PeptideAtlas SRMexperiment library

Cited by 206 publications

References 23 publications

Functional Characterization of the Small Regulatory Subunit PetP from the Cytochrome b6f Complex in Thermosynechococcus elongatus

Functional Characterization of the Small Regulatory Subunit PetP from the Cytochrome b6f Complex in Thermosynechococcus elongatus

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

Applications of targeted proteomics in systems biology and translational medicine

Contact Info

Product

Resources

About

Functional Characterization of the Small Regulatory Subunit PetP from the Cytochrome b₆f Complex in Thermosynechococcus elongatus

Functional Characterization of the Small Regulatory Subunit PetP from the Cytochrome b₆f Complex in Thermosynechococcus elongatus