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Refinements To Label Free Proteome Quantitation: How To Deal With Peptides Shared By Multiple Proteins.

Y. Zhang, Zhihui Wen, M. Washburn, L. Florens
Published 2010 · Chemistry, Medicine

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Quantitative shotgun proteomics is dependent on the detection, identification, and quantitative analysis of peptides. An issue arises with peptides that are shared between multiple proteins. What protein did they originate from and how should these shared peptides be used in a quantitative proteomics workflow? To systematically evaluate shared peptides in label-free quantitative proteomics, we devised a well-defined protein sample consisting of known concentrations of six albumins from different species, which we added to a highly complex yeast lysate. We used the spectral counts based normalized spectral abundance factor (NSAF) as the starting point for our analysis and compared an exhaustive list of possible combinations of parameters to determine what was the optimal approach for dealing with shared peptides and shared spectral counts. We showed that distributing shared spectral counts based on the number of unique spectral counts led to the most accurate and reproducible results.



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10.1371/journal.pone.0155492
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J. Gilmore (2016)
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Justin W. Mabin (2018)
10.1039/c2mt20017a
A systems approach implicates nuclear receptor targeting in the Atp7b(-/-) mouse model of Wilson's disease.
P. Wilmarth (2012)
10.1021/pr200133p
Protein Database and Quantitative Analysis Considerations when Integrating Genetics and Proteomics to Compare Mouse Strains
Suzanne S. Fei (2011)
10.1099/mgen.0.000327
The chromatin bound proteome of the human malaria parasite
G. Batugedara (2020)
10.1038/srep08530
Proteins interacting with cloning scars: a source of false positive protein-protein interactions
C. S. Banks (2015)
10.1038/srep43845
Identification of Topological Network Modules in Perturbed Protein Interaction Networks
Mihaela E. Sardiu (2017)
10.1371/journal.pone.0167535
Trio, a Rho Family GEF, Interacts with the Presynaptic Active Zone Proteins Piccolo and Bassoon
Ryan Terry-Lorenzo (2016)
10.1021/acs.jproteome.6b00366
Dynamic and Combinatorial Landscape of Histone Modifications during the Intraerythrocytic Developmental Cycle of the Malaria Parasite.
A. Saraf (2016)
Summary of Adducted Residues by Anesthetic Photoaffinity Ligands Using Amino Acid Sequencing Methods
Kellie A. Woll (2016)
10.1101/2020.06.06.138156
The histone methyltransferase SETD2 couples transcription and splicing by engaging pre-mRNA processing factors through its SHI domain
Saikat Bhattacharya (2020)
10.1021/pr3010293
Dynamics of the striped bass (Morone saxatilis) ovary proteome reveal a complex network of the translasome.
B. Reading (2013)
Development and Application of Novel Electron Transfer Dissociation-based Technologies for Proteomics
Christian Frese (2013)
Title : An extracellular cysteine-rich protein kinase associates with a membrane 16 immune complex and is required for cell death 17 18 Authors :
K. A. Yadeta (2016)
10.1016/j.molcel.2016.01.004
Antisense Transcripts Delimit Exonucleolytic Activity of the Mitochondrial 3' Processome to Generate Guide RNAs.
T. Suematsu (2016)
10.1016/J.ENVEXPBOT.2018.10.024
Comparative physiological and leaf proteomic analyses revealed the tolerant and sensitive traits to drought stress in two wheat parental lines and their F6 progenies
M. Nemati (2019)
10.1128/IAI.00040-11
Proteomics and Pathway Analyses of the Milk Fat Globule in Sheep Naturally Infected by Mycoplasma agalactiae Provide Indications of the In Vivo Response of the Mammary Epithelium to Bacterial Infection ‡
M. Addis (2011)
10.7554/eLife.49677
Ataxin-7 and Non-stop coordinate SCAR protein levels, subcellular localization, and actin cytoskeleton organization
Veronica Cloud (2019)
10.1016/B978-0-12-384890-1.00011-X
Proteomics and Host—Pathogen Interactions
D. Biron (2010)
10.1002/pmic.201100537
Computational and informatics strategies for identification of specific protein interaction partners in affinity purification mass spectrometry experiments
A. Nesvizhskii (2012)
10.1128/EC.00082-13
Novel Thioredoxin-Like Proteins Are Components of a Protein Complex Coating the Cortical Microtubules of Toxoplasma gondii
J. Liu (2013)
10.1074/mcp.M111.011544
Characterization of a Highly Conserved Histone Related Protein, Ydl156w, and Its Functional Associations Using Quantitative Proteomic Analyses*
J. Gilmore (2011)
10.1101/gad.271429.115
The Enok acetyltransferase complex interacts with Elg1 and negatively regulates PCNA unloading to promote the G1/S transition.
Fu Huang (2016)
10.1038/s41589-018-0217-y
A chemoproteomic portrait of the oncometabolite fumarate
R. A. Kulkarni (2019)
10.1021/acs.jproteome.9b00373
Biochemical Reduction of the Topology of the Diverse WDR76 Protein Interactome.
G. Dayebgadoh (2019)
10.1186/s12870-016-0797-1
Single-cell-type quantitative proteomic and ionomic analysis of epidermal bladder cells from the halophyte model plant Mesembryanthemum crystallinum to identify salt-responsive proteins
B. Barkla (2016)
10.1002/pmic.201300513
Analysis of the interactome of ribosomal protein S19 mutants
M. Caterino (2014)
10.1080/19491034.2018.1469351
Analysis of RNA-Seq datasets reveals enrichment of tissue-specific splice variants for nuclear envelope proteins
Charlotte Capitanchik (2018)
10.1016/J.SMALLRUMRES.2012.07.024
Characterization of size and composition of milk fat globules from Sarda and Saanen dairy goats
S. Pisanu (2013)
10.1371/journal.pone.0104962
An Easy and Efficient Method for Native and Immunoreactive Echinococcus granulosus Antigen 5 Enrichment from Hydatid Cyst Fluid
D. Pagnozzi (2014)
10.1021/cr3003533
Protein analysis by shotgun/bottom-up proteomics.
Yaoyang Zhang (2013)
10.1021/pr4006266
Proteomic analysis of human keratinocyte response to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) exposure.
Q. Hu (2013)
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