MRMaid 2.0: Mining PRIDE for Evidence-Based SRM Transitions

Fan, Jun; Mohareb, Fady; Bond, Nicholas J.; Lilley, Kathryn S.; Bessant, Conrad

doi:10.1089/omi.2011.0143

Cited by 14 publications

(9 citation statements)

References 17 publications

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“…A mentioned already, GPMDB and PeptideAtlas provide already this functionality. Data from PRIDE is being used by the MRMAID resource, with the same purpose in mind [ 127 ]. Another popular data reuse is the building of spectral libraries.…”

Section: Data Reuse From Public Resourcesmentioning

confidence: 99%

Making proteomics data accessible and reusable: Current state of proteomics databases and repositories

et al. 2015

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Compared to other data-intensive disciplines such as genomics, public deposition and storage of MS-based proteomics, data are still less developed due to, among other reasons, the inherent complexity of the data and the variety of data types and experimental workflows. In order to address this need, several public repositories for MS proteomics experiments have been developed, each with different purposes in mind. The most established resources are the Global Proteome Machine Database (GPMDB), PeptideAtlas, and the PRIDE database. Additionally, there are other useful (in many cases recently developed) resources such as ProteomicsDB, Mass Spectrometry Interactive Virtual Environment (MassIVE), Chorus, MaxQB, PeptideAtlas SRM Experiment Library (PASSEL), Model Organism Protein Expression Database (MOPED), and the Human Proteinpedia. In addition, the ProteomeXchange consortium has been recently developed to enable better integration of public repositories and the coordinated sharing of proteomics information, maximizing its benefit to the scientific community. Here, we will review each of the major proteomics resources independently and some tools that enable the integration, mining and reuse of the data. We will also discuss some of the major challenges and current pitfalls in the integration and sharing of the data.

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Section: Data Reuse From Public Resourcesmentioning

confidence: 99%

Making proteomics data accessible and reusable: Current state of proteomics databases and repositories

et al. 2015

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“…In our previous paper [4], we have reviewed a few of these, including ESP predictor [15], Peptide Sieve [16], and PepFly [17,18], PeptideAtlas [8,19] PABST (Peptide Atlas Best SRM Transition Tool) [7,13,8,20], Automated and Targeted Analysis with Quantitative SRM-ATAQS [21], MRMaid, [22], GPMDB MRM Worksheet [23], SRM/MRMAtlas [24,25], TIQAM [26,27] (used in ATAQS workflow), Skyline [28,29], and TPP-MaRiMba [30,31].…”

Section: Related Workmentioning

confidence: 99%

An extensive library of surrogate peptides for all human proteins

Mohammed

Borchers

2015

Journal of Proteomics

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“…MRMaid [44, 45] is part of the Proteosuite software suite. It uses spectra from EBI’s PRIDE database and sequence data from UniProt to suggest an MRM assay for a given protein.…”

Section: Assay Developmentmentioning

confidence: 99%

Review of software tools for design and analysis of large scale MRM proteomic datasets

Colangelo

Chung

Bruce

et al. 2013

Methods

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Selective or Multiple Reaction monitoring (SRM/MRM) is a liquid-chromatography (LC)/tandem-mass spectrometry (MS/MS) method that enables the quantitation of specific proteins in a sample by analyzing precursor ions and the fragment ions of their selected tryptic peptides. Instrumentation software has advanced to the point that thousands of transitions (pairs of primary and secondary m/z values) can be measured in a triple quadrupole instrument coupled to an LC, by a well-designed scheduling and selection of m/z windows. The design of a good MRM assay relies on the availability of peptide spectra from previous discovery-phase LC-MS/MS studies. The tedious aspect of manually developing and processing MRM assays involving thousands of transitions has spurred to development of software tools to automate this process. Software packages have been developed for project management, assay development, assay validation, data export, peak integration, quality assessment, and biostatistical analysis. No single tool provides a complete end-to-end solution, thus this article reviews the current state and discusses future directions of these software tools in order to enable researchers to combine these tools for a comprehensive targeted proteomics workflow.

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MRMaid 2.0: Mining PRIDE for Evidence-Based SRM Transitions

Cited by 14 publications

References 17 publications

Making proteomics data accessible and reusable: Current state of proteomics databases and repositories

Making proteomics data accessible and reusable: Current state of proteomics databases and repositories

An extensive library of surrogate peptides for all human proteins

Review of software tools for design and analysis of large scale MRM proteomic datasets

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