2DB: a Proteomics database for storage, analysis, presentation, and retrieval of information from mass spectrometric experiments

Allmer, Jens; Kuhlgert, Sebastian; Hippler, Michael

doi:10.1186/1471-2105-9-302

Cited by 8 publications

(10 citation statements)

References 31 publications

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“…MSMAG, developed in this study, depends on an installation of the 2DB database application (Allmer et al 2008), either locally or on a web server. The 2DB software is available at no charge with source code openly available.…”

Section: Methodsmentioning

confidence: 99%

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Label-free quantitation, an extension to 2DB

Allmer

2009

Amino Acids

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Determining the differential expression of proteins under different conditions is of major importance in proteomics. Since mass spectrometry-based proteomics is often used to quantify proteins, several labelling strategies have been developed. While these are generally more precise than label-free quantitation approaches, they imply specifically designed experiments which also require knowledge about peptides that are expected to be measured and need to be modified. We recently designed the 2DB database which aids storage, analysis, and publication of data from mass spectrometric experiments to identify proteins. This database can aid identifying peptides which can be used for quantitation. Here an extension to the database application, named MSMAG, is presented which allows for more detailed analysis of the distribution of peptides and their associated proteins over the fractions of an experiment. Furthermore, given several biological samples in the database, label-free quantitation can be performed. Thus, interesting proteins, which may warrant further investigation, can be identified en passant while performing high-throughput proteomics studies.

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Section: Methodsmentioning

confidence: 99%

“…Many software tools for this purpose have been reviewed in Mueller et al (2008). We recently developed 2DB, a database to hold, study, and publish proteomics data, as generated from MS experiments (Allmer et al 2008). An automated quantitation facility has not been available in the 2DB software but is presented herein.…”

Section: Introductionmentioning

confidence: 99%

Label-free quantitation, an extension to 2DB

Allmer

2009

Amino Acids

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“…Both can be used for error tolerant database search while de novo sequence predictions can also be used standalone. Integrating information from de novo sequencing, database search and additional resources can increase the confidence in each protein identification [100].…”

Section: Data Integrationmentioning

confidence: 99%

Algorithms for thede novosequencing of peptides from tandem mass spectra

Allmer¹

2011

Expert Review of Proteomics

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110

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Proteomics is the study of the proteins, their time and location dependent expression profiles as well as their modifications and interactions. Mass spectrometry is useful to investigate many of the questions asked in proteomics. Typically database search methods are employed to identify proteins from complex mixtures. However, often databases are not available or despite their availability some sequences are not readily found therein. To overcome this problem de novo sequencing can be used to directly assign a peptide sequence to an MS/MS spectrum. Many algorithms have been proposed for de novo sequencing and a selection of them is detailed in this review. Although a standard accuracy measure has not been agreed upon in the field, relative algorithm performance is discussed. The current state of the de novo sequencing is assessed thereafter and finally, examples are used to construct possible future perspectives of the field. Running title:De novo sequencing of MS/MS spectra

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“…At least MSMAG (Allmer 2010) in conjunction with 2DB (Allmer et al 2008) is able to relatively quantify one or more arbitrary labels or PTMs without further modifications.…”

Section: Quantifying Ptms With Lc-ms/msmentioning

confidence: 99%

Existing bioinformatics tools for the quantitation of post-translational modifications

Allmer

2010

Amino Acids

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Mass spectrometry (MS)-based proteomics, by itself, is a vast and complex area encompassing various mass spectrometers, different spectra, and search result representations. When the aim is quantitation performed in different scanning modes at different MS levels, matters become additionally complex. Quantitation of post-translational modifications (PTM) represents the greatest challenge among these endeavors. Many different approaches to quantitation have been described and some of these can be directly applied to the quantitation of PTMs. The amount of data produced via MS, however, makes manual data interpretation impractical. Therefore, specialized software tools meet this challenge. Any software currently able to quantitate differentially labeled samples may theoretically be adapted to quantitate differential PTM expression among samples as well. Due to the heterogeneity of mass spectrometry-based proteomics; this review will focus on quantitation of PTM using liquid chromatography followed by one or more stages of mass spectrometry. Currently available free software, which either allow analysis of PTM or are easily adaptable for this purpose, is briefly reviewed in this paper. Selected studies, especially those related to phosphoproteomics, shall be used to highlight the current ability to quantitate PTMs.

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2DB: a Proteomics database for storage, analysis, presentation, and retrieval of information from mass spectrometric experiments

Cited by 8 publications

References 31 publications

Label-free quantitation, an extension to 2DB

Label-free quantitation, an extension to 2DB

Algorithms for thede novosequencing of peptides from tandem mass spectra

Existing bioinformatics tools for the quantitation of post-translational modifications

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