PhosCalc: a tool for evaluating the sites of peptide phosphorylation from mass spectrometer data.

BMC Research Notes
Daniel MacLeanAlexandra Me Jones

Abstract

We have created a software implementation of a published and verified method for assigning probabilities to potential phosphorylation sites on peptides using mass spectrometric data. Our tool, named PhosCalc, determines the number of possible phosphorylation sites and calculates the theoretical masses for the b and y fragment ions of a user-provided peptide sequence. A corresponding user-provided mass spectrum is examined to determine which putative b and y ions have support in the spectrum and a probability score is calculated for each combination of phosphorylation sites. We test the implementation using spectra of phosphopeptides from bovine beta-casein and we compare the results from the implementation to those from manually curated and verified phosphopeptides from our own experiments. We find that the PhosCalc scores are capable of helping a user to identify phosphorylated sites and can remove a bottleneck in high throughput proteomics analyses. PhosCalc is available as a web-based interface for examining up to 100 peptides and as a downloadable tool for examining larger numbers of peptides. PhosCalc can be used to speed up identification of phosphorylation sites and can be easily integrated into data handling pipelines m...Continue Reading

References

Sep 2, 2004·Nature Reviews. Molecular Cell Biology·Hanno Steen, Matthias Mann
Sep 7, 2004·Proceedings of the National Academy of Sciences of the United States of America·Jesper V Olsen, Matthias Mann
Oct 13, 2006·Nature Biotechnology·Ole N Jensen
Jun 26, 2007·Molecular & Cellular Proteomics : MCP·Totte NiittyläWaltraud X Schulze
Aug 20, 2008·BMC Research Notes·Daniel MacLeanAlexandra Me Jones

❮ Previous
Next ❯

Citations

Nov 3, 2009·Nucleic Acids Research·Pawel DurekWaltraud X Schulze
May 17, 2011·Nucleic Acids Research·Anastasia AlexandridouGeorge Spyrou
Nov 1, 2011·Plant & Cell Physiology·Hirofumi NakagamiKen Shirasu
Aug 20, 2008·BMC Research Notes·Daniel MacLeanAlexandra Me Jones
Feb 28, 2009·Journal of Proteomics·Alexandra M E JonesScott C Peck
Mar 13, 2016·Journal of Experimental Botany·Sacha Baginsky
Aug 19, 2009·Proteomics·Jun ItoJoshua L Heazlewood
Jul 14, 2010·Rapid Communications in Mass Spectrometry : RCM·Yutaka KyonoYasushi Ishihama
Sep 14, 2010·Wiley Interdisciplinary Reviews. Systems Biology and Medicine·Nurhan OzluJudith A J Steen
Nov 19, 2009·The Plant Journal : for Cell and Molecular Biology·Jose R GutierrezJohn P Rathjen
Mar 10, 2016·Expert Review of Proteomics·Chi Yuet X'avia ChanWei-Jun Qian
Oct 26, 2012·Journal of Proteome Research·Mathias VandenbogaertDelphine Pflieger
Jun 7, 2012·Journal of Proteome Research·Mathieu CourcellesPierre Thibault
Sep 6, 2011·Analytical Chemistry·Takeshi MasudaYasushi Ishihama
Oct 16, 2014·Journal of Experimental Botany·Qingtao LuSacha Baginsky
Sep 12, 2012·Molecular & Cellular Proteomics : MCP·Koshi ImamiYasushi Ishihama
Mar 13, 2014·Molecular & Cellular Proteomics : MCP·Cuauhtemoc Licona-CassaniLars K Nielsen
Sep 17, 2013·Molecular & Cellular Proteomics : MCP·Philippe P Roux, Pierre Thibault
Jul 22, 2019·Scientific Reports·Naoyuki SugiyamaYasushi Ishihama
Mar 24, 2012·Plant Physiology·Louis J MeyerJay J Thelen
Aug 6, 2015·Plant Physiology·Qintao LuSacha Baginsky
May 1, 2019·Journal of Proteome Research·Mio IwasakiMasato Nakagawa
Jul 11, 2019·Journal of Proteome Research·David D ShteynbergRobert L Moritz

❮ Previous
Next ❯

Software Mentioned

Winzip
MS Excel
Windows
Ascore
dta
MacOS X
Sequest
MSQuant
MASCOT
Perl

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.