PRIDE: new developments and new datasets

Jones, Philip; Côté, Richard G.; Cho, Sang Yun; Klie, Sebastian; Martens, Lennart; Quinn, Antony F.; Thorneycroft, David; Hermjakob, Henning

doi:10.1093/nar/gkm1021

Cited by 131 publications

(118 citation statements)

References 28 publications

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“…However, protocols or modification within protocols had to be annotated. Data [8,9]) serving as reference data for future analysis.…”

Section: Introductionmentioning

confidence: 99%

HUPO Brain Proteome Project: Summary of the pilot phase and introduction of a comprehensive data reprocessing strategy

Hamacher¹,

Apweiler²,

Arnold³

et al. 2006

Proteomics

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The Human Proteome Organisation (HUPO) initiated several projects focusing on the proteome analysis of distinct human organs. The Brain Proteome Project (BPP) is the initiative dedicated to the brain, its development and correlated diseases. Two pilot studies have been performed aiming at the comparison of techniques, laboratories and approaches. With the help of the results gained, objective data submission, storage and reprocessing workflow have been established. The biological relevance of the data will be drawn from the inter-laboratory comparisons as well as from the re-calculation of all data sets submitted by the different groups. In the following, results of the single groups as well as the centralised reprocessing effort will be summarised and compared, showing the added value of this concerted work.

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“…However, protocols or modification within protocols had to be annotated. Data [8,9]) serving as reference data for future analysis.…”

Section: Introductionmentioning

confidence: 99%

HUPO Brain Proteome Project: Summary of the pilot phase and introduction of a comprehensive data reprocessing strategy

Hamacher¹,

Apweiler²,

Arnold³

et al. 2006

Proteomics

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“…We identified 1,429 phosphoproteins and 3,029 unique phosphopeptides at a false discovery rate of 0.44% for MASCOT and 0.12% for INSPECT searches and established the exact sites of phosphorylation in 2,349 peptides (Table I; Supplemental Tables S1-S3). Details of peptide assignment, together with the original spectra, are publicly available in the PRIDE database (www.ebi.ac.uk/pride/prideMart.do; Jones et al, 2008). Our data set is comparable in size to the phosphoproteome data set reported recently by Sugiyama et al (2008).…”

Section: The Arabidopsis Phosphoproteomementioning

confidence: 99%

Large-Scale Arabidopsis Phosphoproteome Profiling Reveals Novel Chloroplast Kinase Substrates and Phosphorylation Networks

et al. 2009

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We have characterized the phosphoproteome of Arabidopsis (Arabidopsis thaliana) seedlings using high-accuracy mass spectrometry and report the identification of 1,429 phosphoproteins and 3,029 unique phosphopeptides. Among these, 174 proteins were chloroplast phosphoproteins. Motif-X (motif extractor) analysis of the phosphorylation sites in chloroplast proteins identified four significantly enriched kinase motifs, which include casein kinase II (CKII) and proline-directed kinase motifs, as well as two new motifs at the carboxyl terminus of ribosomal proteins. Using the phosphorylation motifs as a footprint for the activity of a specific kinase class, we connected the phosphoproteins with their putative kinases and constructed a chloroplast CKII phosphorylation network. The network topology suggests that CKII is a central regulator of different chloroplast functions. To provide insights into the dynamic regulation of protein phosphorylation, we analyzed the phosphoproteome at the end of day and end of night. The results revealed only minor changes in chloroplast kinase activities and phosphorylation site utilization. A notable exception was ATP synthase b-subunit, which is found phosphorylated at CKII phosphorylation sites preferentially in the dark. We propose that ATP synthase is regulated in cooperation with 14-3-3 proteins by CKII-mediated phosphorylation of ATP synthase b-subunit in the dark.

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“…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.…”

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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

1,107

953

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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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PRIDE: new developments and new datasets

Cited by 131 publications

References 28 publications

HUPO Brain Proteome Project: Summary of the pilot phase and introduction of a comprehensive data reprocessing strategy

HUPO Brain Proteome Project: Summary of the pilot phase and introduction of a comprehensive data reprocessing strategy

Large-Scale Arabidopsis Phosphoproteome Profiling Reveals Novel Chloroplast Kinase Substrates and Phosphorylation Networks

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

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