Using synthetic peptides to benchmark peptide identification software and search parameters for MS/MS data analysis

Quandt, Andreas; Pernas, Lucia Espona; Balaskó, Ákos; Weisser, Hendrik; Brusniak, Mi-Youn; Kunszt, Péter Z.; Aebersold, Ruedi; Malmström, Lars

doi:10.1016/j.euprot.2014.10.001

Cited by 9 publications

(12 citation statements)

References 40 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Analyzing a sufficiently large set of MS2 spectra with different peptide and protein identification (ID) engines, including database search engines, generally gives partially different, often complementary results. 28 To take advantage of this, OpenMS provides the ConsensusID tool, which combines search results on the PSM level from different ID engines. Given ranked lists of PSMs produced by different engines, several algorithms are available to merge and rescore PSMs derived from the same spectrum: similarity scoring based on sequence or fragmentation pattern similarity, 29 ranked voting, or simply using the average or the best score for each peptide.…”

Section: Resultsmentioning

confidence: 99%

Flexible Data Analysis Pipeline for High-Confidence Proteogenomics

Weisser¹,

Wright²,

Mudge³

et al. 2016

J. Proteome Res.

Self Cite

View full text Add to dashboard Cite

Proteogenomics leverages information derived from proteomic data to improve genome annotations. Of particular interest are “novel” peptides that provide direct evidence of protein expression for genomic regions not previously annotated as protein-coding. We present a modular, automated data analysis pipeline aimed at detecting such “novel” peptides in proteomic data sets. This pipeline implements criteria developed by proteomics and genome annotation experts for high-stringency peptide identification and filtering. Our pipeline is based on the OpenMS computational framework; it incorporates multiple database search engines for peptide identification and applies a machine-learning approach (Percolator) to post-process search results. We describe several new and improved software tools that we developed to facilitate proteogenomic analyses that enhance the wealth of tools provided by OpenMS. We demonstrate the application of our pipeline to a human testis tissue data set previously acquired for the Chromosome-Centric Human Proteome Project, which led to the addition of five new gene annotations on the human reference genome.

show abstract

Section: Resultsmentioning

confidence: 99%

Flexible Data Analysis Pipeline for High-Confidence Proteogenomics

Weisser¹,

Wright²,

Mudge³

et al. 2016

J. Proteome Res.

Self Cite

View full text Add to dashboard Cite

show abstract

“…In this study, to provide a comprehensive overview of the miracidia proteome, we combined the results of four search engines to assess the MS/MS spectral data. The outcome indicated distinct variations in protein identification dependent on the search engine (see Fig 1B ), which could be attributed to differences in search algorithms and associated parameter settings [ 43 ]. This is supported by a recent benchmark study that used a pool of 20,103 synthetic peptides to evaluate peptide-spectrum matches (PSMs) using two different LCMS systems followed by the analysis with 1,800 different search engine and parameter set combinations [ 43 ].…”

Section: Discussionmentioning

confidence: 99%

“…The outcome indicated distinct variations in protein identification dependent on the search engine (see Fig 1B ), which could be attributed to differences in search algorithms and associated parameter settings [ 43 ]. This is supported by a recent benchmark study that used a pool of 20,103 synthetic peptides to evaluate peptide-spectrum matches (PSMs) using two different LCMS systems followed by the analysis with 1,800 different search engine and parameter set combinations [ 43 ]. That study found that the choice of parameter settings had a large influence on the identification performance of the search engine.…”

Section: Discussionmentioning

confidence: 99%

Proteomic Analysis of the Schistosoma mansoni Miracidium

et al. 2016

View full text Add to dashboard Cite

Despite extensive control efforts, schistosomiasis continues to be a major public health problem in developing nations in the tropics and sub-tropics. The miracidium, along with the cercaria, both of which are water-borne and free-living, are the only two stages in the life-cycle of Schistosoma mansoni which are involved in host invasion. Miracidia penetrate intermediate host snails and develop into sporocysts, which lead to cercariae that can infect humans. Infection of the snail host by the miracidium represents an ideal point at which to interrupt the parasite’s life-cycle. This research focuses on an analysis of the miracidium proteome, including those proteins that are secreted. We have identified a repertoire of proteins in the S. mansoni miracidium at 2 hours post-hatch, including proteases, venom allergen-like proteins, receptors and HSP70, which might play roles in snail-parasite interplay. Proteins involved in energy production and conservation were prevalent, as were proteins predicted to be associated with defence. This study also provides a strong foundation for further understanding the roles that neurohormones play in host-seeking by schistosomes, with the potential for development of novel anthelmintics that interfere with its various life-cycle stages.

show abstract

“…2 ) [65]. Tandem mass spectra were searched against the UniProt _ Oryza sativa (63,195 sequences) concatenated with reverse decoy database.…”

Section: Methodsmentioning

confidence: 99%

Proteome Profile of Starch Granules Purified from Rice (Oryza sativa) Endosperm

et al. 2016

View full text Add to dashboard Cite

Starch is the most important food energy source in cereals. Many of the known enzymes involved in starch biosynthesis are partially or entirely granule-associated in the endosperm. Studying the proteome of rice starch granules is critical for us to further understand the mechanisms underlying starch biosynthesis and packaging of starch granules in rice amyloplasts, consequently for the improvement of rice grain quality. In this article, we developed a protocol to purify starch granules from mature rice endosperm and verified the quality of purified starch granules by microscopy observations, I2 staining, and Western blot analyses. In addition, we found the phenol extraction method was superior to Tris-HCl buffer extraction method with respect to the efficiency in recovery of starch granule associated proteins. LC-MS/MS analysis showed identification of already known starch granule associated proteins with high confidence. Several proteins reported to be involved in starch synthesis in prior genetic studies in plants were also shown to be enriched with starch granules, either directly or indirectly, in our studies. In addition, our results suggested that a few additional candidate proteins may also be involved in starch synthesis. Furthermore, our results indicated that some starch synthesis pathway proteins are subject to protein acetylation modification. GO analysis and KEGG pathway enrichment analysis showed that the identified proteins were mainly located in plastids and involved in carbohydrate metabolism. This study substantially advances the understanding of the starch granule associated proteome in rice and post translational regulation of some starch granule associated proteins.

show abstract

Using synthetic peptides to benchmark peptide identification software and search parameters for MS/MS data analysis

Cited by 9 publications

References 40 publications

Flexible Data Analysis Pipeline for High-Confidence Proteogenomics

Flexible Data Analysis Pipeline for High-Confidence Proteogenomics

Proteomic Analysis of the Schistosoma mansoni Miracidium

Proteome Profile of Starch Granules Purified from Rice (Oryza sativa) Endosperm

Contact Info

Product

Resources

About