1
|
Abstract
Label-free quantification of shotgun proteomics data is a frequently used strategy, offering high dynamic range, sensitivity, and the ability to compare a high number of samples without additional labeling effort. Here, we present a bioinformatics approach that significantly improves label-free quantification results. We employ Percolator to assess the quality of quantified peptides. This allows to extract accurate and reliable quantitative results based on false discovery rate. Benchmarking our approach on previously published public data shows that it considerably outperforms currently available algorithms. apQuant is available free of charge as a node for Proteome Discoverer.
Collapse
Affiliation(s)
- Johannes Doblmann
- Research Institute of Molecular Pathology (IMP) , Vienna Biocenter (VBC) , Campus-Vienna-Biocenter 1 , 1030 Vienna , Austria
| | - Frederico Dusberger
- Research Institute of Molecular Pathology (IMP) , Vienna Biocenter (VBC) , Campus-Vienna-Biocenter 1 , 1030 Vienna , Austria
| | - Richard Imre
- Research Institute of Molecular Pathology (IMP) , Vienna Biocenter (VBC) , Campus-Vienna-Biocenter 1 , 1030 Vienna , Austria.,Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA) , Vienna Biocenter (VBC) , Dr. Bohr-Gasse 3 , 1030 Vienna , Austria
| | - Otto Hudecz
- Research Institute of Molecular Pathology (IMP) , Vienna Biocenter (VBC) , Campus-Vienna-Biocenter 1 , 1030 Vienna , Austria.,Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA) , Vienna Biocenter (VBC) , Dr. Bohr-Gasse 3 , 1030 Vienna , Austria
| | - Florian Stanek
- Research Institute of Molecular Pathology (IMP) , Vienna Biocenter (VBC) , Campus-Vienna-Biocenter 1 , 1030 Vienna , Austria
| | - Karl Mechtler
- Research Institute of Molecular Pathology (IMP) , Vienna Biocenter (VBC) , Campus-Vienna-Biocenter 1 , 1030 Vienna , Austria.,Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA) , Vienna Biocenter (VBC) , Dr. Bohr-Gasse 3 , 1030 Vienna , Austria
| | - Gerhard Dürnberger
- Research Institute of Molecular Pathology (IMP) , Vienna Biocenter (VBC) , Campus-Vienna-Biocenter 1 , 1030 Vienna , Austria.,Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA) , Vienna Biocenter (VBC) , Dr. Bohr-Gasse 3 , 1030 Vienna , Austria.,Gregor Mendel Institute of Molecular Plant Biology (GMI) , Vienna Biocenter (VBC) , Dr. Bohr-Gasse 3 , 1030 Vienna , Austria
| |
Collapse
|
2
|
Pichler P, Mazanek M, Dusberger F, Weilnböck L, Huber CG, Stingl C, Luider TM, Straube WL, Köcher T, Mechtler K. SIMPATIQCO: a server-based software suite which facilitates monitoring the time course of LC-MS performance metrics on Orbitrap instruments. J Proteome Res 2012; 11:5540-7. [PMID: 23088386 PMCID: PMC3558011 DOI: 10.1021/pr300163u] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
![]()
While the performance of liquid chromatography (LC) and
mass spectrometry (MS) instrumentation continues to increase, applications
such as analyses of complete or near-complete proteomes and quantitative
studies require constant and optimal system performance. For this
reason, research laboratories and core facilities alike are recommended
to implement quality control (QC) measures as part of their routine
workflows. Many laboratories perform sporadic quality control checks.
However, successive and systematic longitudinal monitoring of system
performance would be facilitated by dedicated automatic or semiautomatic
software solutions that aid an effortless analysis and display of
QC metrics over time. We present the software package SIMPATIQCO (SIMPle AuTomatIc Quality COntrol) designed
for evaluation of data from LTQ Orbitrap, Q-Exactive, LTQ FT, and
LTQ instruments. A centralized SIMPATIQCO server can process QC data
from multiple instruments. The software calculates QC metrics supervising
every step of data acquisition from LC and electrospray to MS. For
each QC metric the software learns the range indicating adequate system
performance from the uploaded data using robust statistics. Results
are stored in a database and can be displayed in a comfortable manner
from any computer in the laboratory via a web browser. QC data can
be monitored for individual LC runs as well as plotted over time.
SIMPATIQCO thus assists the longitudinal monitoring of important QC
metrics such as peptide elution times, peak widths, intensities, total
ion current (TIC) as well as sensitivity, and overall LC–MS
system performance; in this way the software also helps identify potential
problems. The SIMPATIQCO software package is available free of charge.
Collapse
Affiliation(s)
- Peter Pichler
- Research Institute of Molecular Pathology, Vienna, Austria.
| | | | | | | | | | | | | | | | | | | |
Collapse
|