PROTEOIQ Citations

BIOINQUIRE’s software is being used by an array of researchers to answer a wide range of questions. Below you will find a list of the articles in which our software has been used and/or cited.

BIOINQUIRE is committed to continuing development of software that supports the scientific discovery process.


Lukas Kall, John D. Storey, Michael J. MacCoss, William S. Noble.
"Assigning significance to peptides identified by tandem mass spectrometry using decoy databases."
Journal of Proteome Research. 2008,7,29-34.

Eric D. Dodds, Brian H. Clowers, Paul J. Hagerman, Carlito B. Lebrilla.
"Systematic characterization of high mass accuracy influence on false discovery and probability scoring in peptide mass fingerprinting."
Analytical Biochemistry. 2008, 372, 156-166.

Nicholas T. Seyfried, Leanne C. Husentruyt, James A. Atwood III, Qiangwei Xia, Thomas N. Seyfried,, Ron Orlando.
"Up-Regulation of NG2 Proteoglycan and Interferon Induced Transmembrane Proteins 1 and 3 in Mouse Astrocytoma: A Membrane Proteomics Approach."
Cancer Letters, 2008.

Yufeng Shen, Nikola Tolie, Kim K. Hixson, Samuel O. Purvine, Ljiljana Pasa-Tolie, Wei-Jun Qian, Joshua N. Adkins, Ronal J. Moore, Richard D. Smith.
"Proteome-wide identification of proteins and their modifications with decreased ambiguities and improved false discovery rates using unique sequence tags."
Analytical Chemistry. 2008.

Robert L.J. Graham, Ciaren Graham, Geoff McMullan.
"Microbial proteomics: a mass spectrometry primer for biologist."
Microbial cell factories. 2007, 6, 26.

Patrick D. Curtis, James A. Atwood III, Ron Orlando, Lawrence J. Shimkets.
"Proteins associated with the Myxococcus xanthus extracellular matrix."
Journal of Bacteriology. 2007, 189, 7634-7442.

Xinning Jiang, Xiaogang Jiang, Guanghui Han, Mingliang Ye, Hanga Xou.
"Optimization of filtering criterion for SEQUEST database searching to improve proteome coverage in shotgun proteomics."
BMC Bioinformatics. 2007, 8, 323.

Robert L.J. Graham, Mohit K. Sharma, Nigel G. Ternan, D. Brent Weatherly, Rick L. Tarleton, Geoff McMullan.
"A semi-quantitative GeLC-MS analysis of temporal proteome expression in the emerging nosocomial pathogen Ochrobactrum anthropi."
Genome Biology. 2007, 8, R110.

Francesca Forner, Leonard J. Foster, Stefano Toppo.
"Mass spectrometry data analysis in the proteomics era."
Current Bioinformatics. 2007, 2, 63-93.

Alexey I. Nesvizhskii, Olga Vitek, Ruedi Aebersold.
"Analysis and validation of proteomics data generated by tandem mass spectrometry."
Nature Methods. 2007, 4, 787-797.

Wan Yang, Randall L. Woltjer, Izabela Sokal, Catherine Pan, Yan Wang, Mary Brodey, Elaine R. Peskind, James B. Leverenz, Jing Zhang, Daniel P. Perl, Douglas R. Galasko, Thomas J. Montine.
"Quantitative proteomics identifies surfactant-resistant á-Synuclein in cerebral cortex of parkinsonism-dementia complex of guam but not Alzheimer’s disease or progressive supranuclear palsy."
The American Journal of Pathology. 2007, 171, 993-1002.

Sung-Min Ahn, Richard J. Simpson.
"Proteomic strategies for analyzing body fluids."
Humana Press. 2007.

Shaojun Sun, Karen Meyer-Arendt, Brian Eichelberger, Robert Brown, Chia-Yu Yen, William M. Old, Kevin Pierce, Krzysztof J. Cios, Natalie G. Ahn, Katheryn A. Resing.
"Improved Validation of Peptide MS/MS Assignments Using Spectral Intensity Prediction."
Molecular & Cellular Proteomics. 2007, 6, 1-17.

James G. Rohrbough, Linda Breci, Nirav Merchant, Susan Miller, Paul A. Haynes.
"Verification of single-peptide protein identifications by the application of complementary database search algorithms."
Journal of Biomolecular Techniques. 2006, 17, 327-332.

Robert L.J. Graham, Catherin E. Pollock, S. Naomi O’Loughlin, Nigel G. Ternan, D. Brent Weatherly, Philip J. Jackson, Rick L. Tarleton, Geoff McMullan.
"Multidimensional proteomic analysis of the soluble subproteome of the emerging nosocomial pathogen Ochrobactrum anthropi."
Journal of Proteome Research. 2006. 5, 3145-3153.

James A. Atwood III, Todd Minning, Fernanda Ludolf, Arthur Nuccio, D. Brent Weatherly, Gerardo Alverez-Manilla, Rick Tarleton, Ron Orlando.
"Glycoproteomics of Trypanosoma cruzi trypomastigotes using subcellular fractionation, lectin affinity, and stable isotope labeling."
Journal of Proteome Research. 2006, 5, 3376-3384.

Robert L.J. Graham, S. Naomi O’Loughlin, Catherin E. Pollock, Nigel G. Ternan, D. Brent Weatherly, Philip J. Jackson, Rick L. Tarleton, Geoff McMullan.
"A combined shotgun and multidimensional proteomic analysis of the insoluble subproteome of the obligate thermophile, Geobacillus thermoleovaorans T80."
Journal of Proteome Research. 2006, 5, 2465-2473.

James A. Atwood III, Satya S. Sahoo, Gerardo Alverez-Manilla, D. Brent Weatherly, Kumar Kolli, Ron Orlando, William S. York.
"Simple modification of a protein database for mass spectral identification of N-linked glycopeptides."
Rapid Communications in Mass Spectrometry. 2005, 19, 3002-3006.

Rick L. Tarleton.
"New approaches in vaccine development for parasitic infections."
Cellular Microbiology. 2005, 7, 1379-1386.

James A. Atwood III, D. Brent Weatherly, Todd A. Minning, Becky Bundy, Cameron Cavola, Fred R, Opperdoes, Ron Orlando, Rick L. Tarleton.
"The Trypanosoma cruzi proteome."
Science. 2005, 309, 473-476.

D. Brent Weatherly, James A. Atwood III, Todd A. Minning, Cameron Cavola, Rick L. Tarleton, Ron Orlando.
"A heuristic method for assigning a false-discovery rate for protein identifications from Mascot database search results."
Molecular & Cellular Proteomics. 2005, 4, 762-772.