Unbiased statistical analysis for multi-stage proteomic search strategies

Journal of Proteome Research
Logan J EverettStephen R Master

Abstract

"Multi-stage" search strategies have become widely accepted for peptide identification and are implemented in a number of available software packages. We describe limitations of these strategies for validation and decoy-based statistical analyses and demonstrate these limitations using a set of control sample spectra. We propose a solution that corrects the statistical deficiencies and describe its implementation using the open-source software X!Tandem.

References

Jul 30, 2002·Omics : a Journal of Integrative Biology·Andrew KellerEugene Kolker
Nov 8, 2002·Proteomics·David M Creasy, John S Cottrell
Oct 15, 2003·Rapid Communications in Mass Spectrometry : RCM·Robertson Craig, Ronald C Beavis
Nov 25, 2003·Analytical Chemistry·Alexey I NesvizhskiiRuedi Aebersold
Feb 21, 2004·Bioinformatics·Robertson Craig, Ronald C Beavis
May 27, 2006·Molecular Systems Biology·Andrew KellerRuedi Aebersold
Oct 4, 2006·Molecular & Cellular Proteomics : MCP·Michael L NielsenRoman A Zubarev
Dec 7, 2007·Journal of Proteome Research·Lukas KällWilliam Stafford Noble
Dec 11, 2007·Journal of Proteome Research·Lukas KällWilliam Stafford Noble
Dec 11, 2007·Journal of Proteome Research·Hyungwon Choi, Alexey I Nesvizhskii
Dec 28, 2007·Journal of Proteome Research·Hyungwon Choi, Alexey I Nesvizhskii
Jan 5, 2008·Journal of Proteome Research·Brian C SearleAlexey I Nesvizhskii
Nov 1, 1994·Journal of the American Society for Mass Spectrometry·J K EngJ R Yates

❮ Previous
Next ❯

Citations

Feb 5, 2013·Amino Acids·Harald Barsnes, Lennart Martens
Sep 29, 2011·Journal of the American Society for Mass Spectrometry·Nitin GuptaPavel A Pevzner
Feb 4, 2011·Journal of Proteome Research·Marshall Bern, Yong J Kil
Oct 21, 2011·Journal of Proteome Research·Marshall W Bern, Yong J Kil
Dec 22, 2011·Molecular & Cellular Proteomics : MCP·Seungjin NaEunok Paek
Aug 31, 2011·Molecular & Cellular Proteomics : MCP·Jimmy K EngDavid L Tabb
Jun 24, 2010·Omics : a Journal of Integrative Biology·Roger HigdonEugene Kolker
Nov 28, 2012·BMC Bioinformatics·Kyowon JeongNuno Bandeira
Dec 1, 2012·Expert Review of Proteomics·Marc VaudelLennart Martens
Dec 15, 2015·Journal of Proteome Research·Oliver HorlacherMarkus Müller
Oct 3, 2012·Journal of Proteome Research·Paul BlakeleySimon J Hubbard
Jun 4, 2014·Mass Spectrometry Reviews·Seungjin Na, Eunok Paek
Jan 12, 2013·Proteomics·Marc VaudelRené P Zahedi
Mar 29, 2014·Proteomics·Marc VaudelHarald Barsnes
Jun 13, 2012·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Pengyi YangYee Hwa Jean Yang
Jul 13, 2013·Biochimica Et Biophysica Acta·Marc VaudelLennart Martens
Jun 29, 2016·Journal of the American Society for Mass Spectrometry·Mark V IvanovMikhail V Gorshkov
Sep 24, 2015·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Ling JianAndrew J Link
Apr 12, 2012·Journal of Proteome Research·Marc VaudelLennart Martens
Oct 15, 2011·Journal of Proteome Research·Niklaas ColaertLennart Martens
Jun 12, 2019·Scientific Reports·Marco MangiacottiRoberto Sacchi
Mar 23, 2021·Journal of Proteome Research·Paolo CifaniAlex Kentsis
Mar 2, 2017·Journal of Proteome Research·Qiyao LiLloyd M Smith

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.