Dataset Information

Integrated post-experiment monoisotopic mass refinement: an integrated approach to accurately assign monoisotopic precursor masses to tandem mass spectrometric data.

ABSTRACT: Accurate assignment of monoisotopic precursor masses to tandem mass spectrometric (MS/MS) data is a fundamental and critically important step for successful peptide identifications in mass spectrometry based proteomics. Here we describe an integrated approach that combines three previously reported methods of treating MS/MS data for precursor mass refinement. This combined method, "integrated post-experiment monoisotopic mass refinement" (iPE-MMR), integrates steps (1) generation of refined MS/MS data by DeconMSn; (2) additional refinement of the resultant MS/MS data by a modified version of PE-MMR; and (3) elimination of systematic errors of precursor masses using DtaRefinery. iPE-MMR is the first method that utilizes all MS information from multiple MS scans of a precursor ion including multiple charge states, in an MS scan, to determine precursor mass. With the combination of these methods, iPE-MMR increases sensitivity in peptide identification and provides increased accuracy when applied to complex high-throughput proteomics data.

SUBMITTER: Jung HJ

PROVIDER: S-EPMC3019303 | biostudies-literature | 2010 Oct

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Integrated post-experiment monoisotopic mass refinement: an integrated approach to accurately assign monoisotopic precursor masses to tandem mass spectrometric data.

Jung Hee-Jung HJ Purvine Samuel O SO Kim Hokeun H Petyuk Vladislav A VA Hyung Seok-Won SW Monroe Matthew E ME Mun Dong-Gi DG Kim Kyong-Chul KC Park Jong-Moon JM Kim Su-Jin SJ Tolic Nikola N Slysz Gordon W GW Moore Ronald J RJ Zhao Rui R Adkins Joshua N JN Anderson Gordon A GA Lee Hookeun H Camp David G DG Yu Myeong-Hee MH Smith Richard D RD Lee Sang-Won SW

Analytical chemistry 20101001 20

Accurate assignment of monoisotopic precursor masses to tandem mass spectrometric (MS/MS) data is a fundamental and critically important step for successful peptide identifications in mass spectrometry based proteomics. Here we describe an integrated approach that combines three previously reported methods of treating MS/MS data for precursor mass refinement. This combined method, "integrated post-experiment monoisotopic mass refinement" (iPE-MMR), integrates steps (1) generation of refined MS/M ...[more]

PMID: 20863060

Similar Datasets

Project description:The use of unique DNA sequences as a method for taxonomic identification is no longer fundamentally controversial, even though debate continues on the best markers, methods, and technology to use. Although both existing databanks such as GenBank and BOLD, as well as reference taxonomies, are imperfect, in best case scenarios "barcodes" (whether single or multiple, organelle or nuclear, loci) clearly are an increasingly fast and inexpensive method of identification, especially as compared to manual identification of unknowns by increasingly rare expert taxonomists. Because most species on Earth are undescribed, a complete reference database at the species level is impractical in the near term. The question therefore arises whether unidentified species can, using DNA barcodes, be accurately assigned to more inclusive groups such as genera and families-taxonomic ranks of putatively monophyletic groups for which the global inventory is more complete and stable. We used a carefully chosen test library of CO1 sequences from 49 families, 313 genera, and 816 species of spiders to assess the accuracy of genus and family-level assignment. We used BLAST queries of each sequence against the entire library and got the top ten hits. The percent sequence identity was reported from these hits (PIdent, range 75-100%). Accurate assignment of higher taxa (PIdent above which errors totaled less than 5%) occurred for genera at PIdent values >95 and families at PIdent values ? 91, suggesting these as heuristic thresholds for accurate generic and familial identifications in spiders. Accuracy of identification increases with numbers of species/genus and genera/family in the library; above five genera per family and fifteen species per genus all higher taxon assignments were correct. We propose that using percent sequence identity between conventional barcode sequences may be a feasible and reasonably accurate method to identify animals to family/genus. However, the quality of the underlying database impacts accuracy of results; many outliers in our dataset could be attributed to taxonomic and/or sequencing errors in BOLD and GenBank. It seems that an accurate and complete reference library of families and genera of life could provide accurate higher level taxonomic identifications cheaply and accessibly, within years rather than decades.

Project description:ObjectiveTo determine the accuracy of interpretation of a non-contrast MRI protocol in characterizing adnexal masses.Methods and materialsTwo hundred ninety-one patients (350 adnexal masses) who underwent gynecological MRI at our institution between the 1st of January 2008 and the 31st of December 2018 were reviewed. A random subset (102 patients with 121 masses) was chosen to evaluate the reproducibility and repeatability of readers' assessments. Readers evaluated non-contrast MRI scans retrospectively, assigned a 5-point score for the risk of malignancy and gave a specific diagnosis. The reference standard for the diagnosis was histopathology or at least one-year imaging follow-up. Diagnostic accuracy of the non-contrast MRI score was calculated. Inter- and intra-reader agreement was analyzed with Cohen's kappa statistics.ResultsThere were 53/350 (15.1%) malignant lesions in the whole cohort and 20/121 (16.5%) malignant lesions in the random subset. Good agreement between readers was found for the non-contrast MRI score (к = 0.73, 95% confidence interval [CI] 0.58-0.86) whilst the intra-reader agreement was excellent (к = 0.81, 95% CI 0.70-0.88). The non-contrast MRI score value of ≥ 4 was associated with malignancy with a sensitivity of 84.9%, a specificity of 95.9%, an accuracy of 94.2% and a positive likelihood ratio of 21 (area under the receiver operating curve 0.93, 95% CI 0.90-0.96).ConclusionAdnexal mass characterization on MRI without the administration of contrast medium has a high accuracy and excellent inter- and intra-reader agreement. Our results suggest that non-contrast studies may offer a reasonable diagnostic alternative when the administration of intravenous contrast medium is not possible.Key points• A non-contrast pelvic MRI protocol may allow the characterization of adnexal masses with high accuracy. • The non-contrast MRI score may be used in clinical practice for differentiating benign from malignant adnexal lesions when the lack of intravenous contrast medium precludes analysis with the O-RADS MRI score.

Dataset Information

Integrated post-experiment monoisotopic mass refinement: an integrated approach to accurately assign monoisotopic precursor masses to tandem mass spectrometric data.

Publications

Integrated post-experiment monoisotopic mass refinement: an integrated approach to accurately assign monoisotopic precursor masses to tandem mass spectrometric data.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets