Name
Title | ||
|---|---|---|
DIANA--algorithmic improvements for analysis of data-independent acquisition MS data. |
Abstract | ||
|---|---|---|
Motivation: Data independent acquisition mass spectrometry has emerged as a reproducible and sensitive alternative in quantitative proteomics, where parsing the highly complex tandem mass spectra requires dedicated algorithms. Recently, targeted data extraction was proposed as a novel analysis strategy for this type of data, but it is important to further develop these concepts to provide quality-controlled, interference-adjusted and sensitive peptide quantification. Results: We here present the algorithm DIANA and the classifier PyProphet, which are based on new probabilistic sub-scores to classify the chromatographic peaks in targeted data-independent acquisition data analysis. The algorithm is capable of providing accurate quantitative values and increased recall at a controlled false discovery rate, in a complex gold standard dataset. Importantly, we further demonstrate increased confidence gained by the use of two complementary data-independent acquisition targeted analysis algorithms, as well as increased numbers of quantified peptide precursors in complex biological samples. Availability and implementation: DIANA is implemented in scala and python and available as open source (Apache 2.0 license) or precompiled binaries from http://quantitativeproteomics.org/diana. PyProphet can be installed from PyPi (https://pypi.python.org/pypi/pyprophet). Supplementary information: Supplementary data are available at Bioinformatics online. |
Year | DOI | Venue |
|---|---|---|
2015 | 10.1093/bioinformatics/btu686 | BIOINFORMATICS |
Field | DocType | Volume |
Data mining,Data analysis,Computer science,Quantitative proteomics,Mass spectrum,Data-independent acquisition,Data extraction,Mass spectrometry,Parsing,Bioinformatics | Journal | 31 |
Issue | ISSN | Citations |
4 | 1367-4803 | 1 |
PageRank | References | Authors |
0.46 | 2 | 7 |
Name | Order | Citations | PageRank |
|---|---|---|---|
| Johan Teleman | 1 | 1 | 0.46 |
| Hannes L. Röst | 2 | 2 | 1.17 |
| George Rosenberger | 3 | 1 | 0.80 |
| Uwe Schmitt | 4 | 1 | 0.46 |
| Lars Malmström | 5 | 65 | 7.19 |
| Johan Malmström | 6 | 24 | 2.00 |
| Fredrik Levander | 7 | 1 | 0.46 |