ArticleAnalytical chemistry2011
Preview: a program for surveying shotgun proteomics tandem mass spectrometry data.
Article in Analytical chemistry, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Automatic Selection of Search Parameter Values for Mass Spectrometry-Based Search Engines.Journal of proteome research · 2026Article
- UDP-glucose dehydrogenase expression is upregulated following EMT and differentially affects intracellular glycerophosphocholine and acetylaspartate levels in breast mesenchymal cell lines.Molecular oncology · 2022Article
- Influence of Post-Translational Modifications on Protein Identification in Database Searches.ACS omega · 2021Article
- Exercise training reverses cancer-induced oxidative stress and decrease in muscle COPS2/TRIP15/ALIEN.Molecular metabolism · 2020Article
- Bioinformatics Methods for Mass Spectrometry-Based Proteomics Data Analysis.International journal of molecular sciences · 2020Review
- Semiautomated glycoproteomics data analysis workflow for maximized glycopeptide identification and reliable quantification.Beilstein journal of organic chemistry · 2020Article
- Targeting the non-canonical roles of PCNA modifies and increases the response to targeted anti-cancer therapy.Oncotarget · 2019Article
- Changes in cellular signaling proteins in extracts from A549, H460, and U2OS cells treated with cisplatin or docetaxel.Data in brief · 2017Article
- Param-Medic: A Tool for Improving MS/MS Database Search Yield by Optimizing Parameter Settings.Journal of proteome research · 2017Article
- Influence of carboxylation on osteocalcin detection by mass spectrometry.Rapid communications in mass spectrometry : RCM · 2016Article
- Comparative Analysis of Label-Free and 8-Plex iTRAQ Approach for Quantitative Tissue Proteomic Analysis.PloS one · 2015Article
- De novo correction of mass measurement error in low resolution tandem MS spectra for shotgun proteomics.Journal of the American Society for Mass Spectrometry · 2012Article
- Two-dimensional target decoy strategy for shotgun proteomics.Journal of proteome research · 2011Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
Database search programs for peptide identification by tandem mass spectrometry ask their users to set various parameters, including precursor and fragment mass tolerances, digestion specificity, and allowed types of modifications. Even proteomics experts with detailed knowledge of their samples may find it difficult to make these choices without significant investigation, and poor choices can lead to missed identifications and misleading results. Here we describe a program called Preview that analyzes a set of mass spectra for mass errors, digestion specificity, and known and unknown modifications, thereby facilitating parameter selection. Moreover, Preview optionally recalibrates mass over charge measurements, leading to further improvement in identification results. In a study of Bruton's tyrosine kinase, we find that the use of Preview improved the number of confidently identified mass spectra and phosphorylation sites by about 50%.
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