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PeptideWitch–A Software Package to Produce High-Stringency Proteomics Data Visualizations from Label-Free Shotgun Proteomics Data

David C. L. Handler, Flora Cheng, Abdulrahman M. Shathili, Paul A. Haynes
2020 Proteomes  
The program inputs are low stringency protein identification lists output from peptide-to-spectrum matching search engines for 'control' and 'treated' samples.  ...  PeptideWitch is a python-based web module that introduces several key graphical and technical improvements to the Scrappy software platform, which is designed for label-free quantitative shotgun proteomics  ...  Using spectral counts for protein identification and quantitation is not without drawbacks.  ... 
doi:10.3390/proteomes8030021 pmid:32825686 fatcat:y433ix6kdff7bkhmzlkfwjgwcy

PolySTest: Robust statistical testing of proteomics data with missing values improves detection of biologically relevant features [article]

Veit Schwämmle, Christina E Hagensen, Adelina Rogowska-Wrzesinska, Ole N. Jensen
2019 biorxiv/medrxiv   pre-print
AbstractStatistical testing remains one of the main challenges for high-confidence detection of differentially regulated proteins or peptides in large-scale quantitative proteomics experiments by mass  ...  Application of PolySTest to mass spectrometry based large-scale proteomics data obtained from differentiating muscle cells resulted in the rescue of 10%-20% additional proteins in the identified molecular  ...  The full source code is available through https://bitbucket.org/ The muscle data set has been deposited under ProteomeXchange identification number PXD018588 at the PRIDE partner repository [31].  ... 
doi:10.1101/765818 fatcat:tfjdgq5fnfb2dlgqpflqe2xnbm

An assessment of false discovery rates and statistical significance in label-free quantitative proteomics with combined filters

Qingbo Li, Bryan AP Roxas
2009 BMC Bioinformatics  
A FDR is used to gauge the statistical significance of the differentially expressed proteins.  ...  But, confidence is still lacking in using datasets for a biological interpretation without protein sample replicates.  ...  The IS proteins accounted for the variations incurred during sample preparation and down-stream analysis processes.  ... 
doi:10.1186/1471-2105-10-43 pmid:19187558 pmcid:PMC2645366 fatcat:7h32233zbrblbltdkhgc7j766u

Focus on the spectra that matter by clustering of quantification data in shotgun proteomics [article]

Matthew The, Lukas Käll
2018 bioRxiv   pre-print
Quandenser/Triqler outperformed the state-of-the-art method MaxQuant/Perseus, consistently reporting more differentially abundant proteins at 5% FDR: 123 vs. 117 true positives with 0 vs. 25 false positives  ...  Compellingly, in all three clinical datasets investigated, the differentially abundant proteins showed enrichment for functional annotation terms.The source code and binary packages for all major operating  ...  We used the proteins identified at 5% protein-level identification FDR as the background set and thresholded the significant terms at a 5% Benjamin-Hochberg corrected FDR.  ... 
doi:10.1101/488015 fatcat:f6ygowhzo5crxne7p3binc2mma

Focus on the spectra that matter by clustering of quantification data in shotgun proteomics

Matthew The, Lukas Käll
2020 Nature Communications  
Quandenser+Triqler outperforms the state-of-the-art method MaxQuant+Perseus, consistently reporting more differentially abundant proteins for all tested datasets.  ...  Here, we propose a quantification-first approach for peptides that reverses the classical identification-first workflow, thereby preventing valuable information from being discarded in the identification  ...  We would like to thank Timothy Bergström, Kungliga Tekniska Högskolan, for writing the Python converter for combining MS1 spectra in the BoxCar runs.  ... 
doi:10.1038/s41467-020-17037-3 pmid:32591519 fatcat:v2gmqlwj3bg4vdqfzijay4zo7y

Cloud Computing Based Immunopeptidomics Utilizing Community Curated Variant Libraries Simplifies and Improves Neo-Antigen Discovery in Metastatic Melanoma

Amol Prakash, Keira E. Mahoney, Benjamin C. Orsburn
2021 Cancers  
Cells presenting peptides with mutated or other non-canonical sequences can be utilized for both targeted therapies and diagnostics.  ...  Unique peptide neo-antigens presented on the cell surface are attractive targets for researchers in nearly all areas of personalized medicine.  ...  Green shows the same plot, but for 0.1% FDR identifications from Bolt.  ... 
doi:10.3390/cancers13153754 fatcat:zm62xr7rhrgjpapqxladbmu54m

A comprehensive and scalable database search system for metaproteomics [article]

Sandip Chatterjee, Gregory Stupp, Sung Kyu (Robin) Park, Jean-Christophe Ducom, John R Yates, Andrew I Su, Dennis W. Wolan
2016 biorxiv/medrxiv   pre-print
, while retaining a high degree of protein identification accuracy, and allowing for a more in-depth characterization of the functional landscape of the samples.  ...  The protein database, proteomics search engine, and the proteomic data files for the 5 microbiome samples characterized and discussed herein are open source and available for use and additional analysis  ...  Shipman for critical suggestions on database generation and performance testing, P. Thuy-Boun for valuable feedback and discussions, and A. Wang, D. Steinmetz, and J.  ... 
doi:10.1101/053975 fatcat:zwqdusqnuzatfiype6xw2oacxu

A comprehensive and scalable database search system for metaproteomics

Sandip Chatterjee, Gregory S. Stupp, Sung Kyu Robin Park, Jean-Christophe Ducom, John R. Yates, Andrew I. Su, Dennis W. Wolan
2016 BMC Genomics  
, while retaining a high degree of protein identification accuracy and allowing for a more in-depth characterization of the functional landscape of the samples.  ...  The protein database, proteomic search engine, and the proteomic data files for the 5 microbiome samples characterized and discussed herein are open source and available for use and additional analysis  ...  Shipman for critical suggestions on database generation and performance testing, P. Thuy-Boun for valuable feedback and discussions, and A. Wang, D. Steinmetz, and J.  ... 
doi:10.1186/s12864-016-2855-3 pmid:27528457 pmcid:PMC4986259 fatcat:yfaoqqmw2jeirp4i7ezecjp7xu

Re-adaption on Earth after Spaceflights Affects the Mouse Liver Proteome

Viktoria Anselm, Svetlana Novikova, Victor Zgoda
2017 International Journal of Molecular Sciences  
Moreover, bile acid secretion may regenerate on Earth due to reconstitution of related transmembrane proteins and CYP superfamily proteins elevated levels seven days after the spaceflight.  ...  Proteomic data analysis provided 12,206 unique peptides and 1086 identified proteins.  ...  Petzuch for thoroughly proof reading this article and Arthur T. Kopylov for supportive idea discussion.  ... 
doi:10.3390/ijms18081763 pmid:28805685 pmcid:PMC5578152 fatcat:xkcg5ehigje3rl4p2klqyuyctu

Mapping the Melanoma Plasma Proteome (MPP) Using Single-Shot Proteomics Interfaced with the WiMT Database

Natália Almeida, Jimmy Rodriguez, Indira Pla Parada, Yasset Perez-Riverol, Nicole Woldmar, Yonghyo Kim, Henriett Oskolas, Lazaro Betancourt, Jeovanis Gil Valdés, K. Barbara Sahlin, Luciana Pizzatti, A. Marcell Szasz (+7 others)
2021 Cancers  
We created a methodology for protein identification known as Wise MS Transfer (WiMT). Melanoma plasma samples from biobank archives were directly analyzed using simple sample preparation.  ...  WiMT is based on MS1 features between several MS runs together with custom protein databases for ID generation.  ...  In addition, we would like to thank Thermo Fisher Scientific for their generous support and Liconic UK and IngaBritt och Arne Lundbergs Forskningsstiftelse for biobanking support.  ... 
doi:10.3390/cancers13246224 pmid:34944842 pmcid:PMC8699267 fatcat:2ravluncezhr5inhelkyv6mvqi

Genome-Wide Analysis of Positively Selected Genes in Seasonal and Non-Seasonal Breeding Species

Yuhuan Meng, Wenlu Zhang, Jinghui Zhou, Mingyu Liu, Junhui Chen, Shuai Tian, Min Zhuo, Yu Zhang, Yang Zhong, Hongli Du, Xiaoning Wang, Jesus E. Maldonado
2015 PLoS ONE  
Identification of these positively-selected genes might help to identify the molecular mechanisms underlying seasonal and non-seasonal reproductive behaviors.  ...  Bruce Lahn for his advice and comments. We also thank BGI-Shenzhen who provided the Chinese rhesus monkey and cynomolgus macaque genomes. Author Contributions  ...  Reciprocal searches were then performed for each species protein sequences relative to human protein sequences.  ... 
doi:10.1371/journal.pone.0126736 pmid:26000771 pmcid:PMC4441472 fatcat:5flitdodxffw7csimsoo34dyw4

EXTRAPOLATIVE DEMONSTRATING OF CATEGORY-1 MELLITUS PERIODS EXPENDING CONTRASTING STATISTICS FOUNDATIONS

Dr Muhammad Usman Sarwar, Dr Maryam Burhan, Dr Amna Nazeer
2021 Zenodo  
Indicators of AI and transition to mellitus were recognized from single foundations expending an integrative AI calculation and component selection based on improvement.  ...  Writers examined 68 offspring: 46 who advanced AI (22/46 progressed to mellitus) and 26 coordinated controls for gender and age.  ...  As a 1st step, we decided on the ideal AI calculation for each category of information (Supplementary Table 3 ).  ... 
doi:10.5281/zenodo.4437166 fatcat:u5esnolapjgbfmkjhqws66e5ve

Accurate Peptide Fragment Mass Analysis: Multiplexed Peptide Identification and Quantification

Chad R. Weisbrod, Jimmy K. Eng, Michael R. Hoopmann, Tahmina Baker, James E. Bruce
2012 Journal of Proteome Research  
A dot product score is calculated against each spectrum in order to generate a score chromatogram used for both identification and quantification.  ...  Thus, FT-ARM is demonstrated to be a novel and complementary data acquisition, identification, and quantification method for the large scale analysis of peptides.  ...  Priska D. von Haller for helpful discussion. Bibliography  ... 
doi:10.1021/pr2008175 pmid:22288382 pmcid:PMC3319072 fatcat:k54ofu734rhzvpu6ijyl5jjpiu

iGEMS: an integrated model for identification of alternative exon usage events

Sanjana Sood, Krzysztof J. Szkop, Asif Nakhuda, Iain J. Gallagher, Carl Murie, Robert J. Brogan, Jaakko Kaprio, Heikki Kainulainen, Philip J. Atherton, Urho M. Kujala, Thomas Gustafsson, Ola Larsson (+1 others)
2016 Nucleic Acids Research  
In conclusion, iGEMS is a robust method for identification of AEU while the variety of exon usage between human tissues is 5-10 times more prevalent than reported by the Genotype-Tissue Expression consortium  ...  DNA microarrays and RNAseq are complementary methods for studying RNA molecules.  ...  The authors would like to thank Liam Good and Valentina Gburick for their input into the cell biology studies.  ... 
doi:10.1093/nar/gkw263 pmid:27095197 pmcid:PMC4914109 fatcat:i4y5pwfdg5dgtm7iljciuk2d4i

PREDICTIVE MODELLING OF TYPE I DIABETES STAGES USING DISPARATE DATA SOURCES

Dr Muhammad Numan Qayyum, Dr Anam Nisar, Dr Resham Sitara
2020 Zenodo  
Indicators of AI and transition to diabetes were recognized from single sources using an integrative AI calculation and component selection based on improvement.  ...  Our integrative methodology predicted AI (AUC 0.94) and diabetes progression (AUC 0.93) for standard cross-approval.  ...  Grouped by: mother with type 1 diabetes, other FDR (sibling or father) or no FDR. 99 Ascorbate Metabolite Antioxidant and coenzyme 98 Age (years) Metadata Age at T1 100 SSRP1 Protein The  ... 
doi:10.5281/zenodo.3741997 fatcat:easpp6jkqrhspcnlm5q4lakvdi
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