A large, consistent plasma proteomics data set from prospectively collected breast cancer patient and healthy volunteer samples

[1]  T. Siddique,et al.  Informatics-assisted Protein Profiling in a Transgenic Mouse Model of Amyotrophic Lateral Sclerosis*S , 2006, Molecular & Cellular Proteomics.

[2]  U. Stenman,et al.  Prostate-specific antigen forms a complex with and cleaves alpha 1-protease inhibitor in vitro. , 1997, The Prostate.

[3]  E. Diamandis,et al.  Cancer biomarkers: can we turn recent failures into success? , 2010, Journal of the National Cancer Institute.

[4]  Leepika Tuli,et al.  LC-MS Based Detection of Differential Protein Expression. , 2009, Journal of proteomics & bioinformatics.

[5]  J. Derisi,et al.  Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise , 2006, Nature.

[6]  D. N. Perkins,et al.  Probability‐based protein identification by searching sequence databases using mass spectrometry data , 1999, Electrophoresis.

[7]  K. Koike,et al.  Limitation of immunoaffinity column for the removal of abundant proteins from plasma in quantitative plasma proteomics. , 2009, Biomedical chromatography : BMC.

[8]  D. James,et al.  American Biotechnology Laboratory , 2002 .

[9]  R. Dean,et al.  Direct comparison of stable isotope labeling by amino acids in cell culture and spectral counting for quantitative proteomics. , 2010, Analytical chemistry.

[10]  S. Hanash,et al.  Mining the plasma proteome for cancer biomarkers , 2008, Nature.

[11]  Gilbert S Omenn,et al.  An evaluation, comparison, and accurate benchmarking of several publicly available MS/MS search algorithms: Sensitivity and specificity analysis , 2005, Proteomics.

[12]  M. Mann,et al.  A high confidence , manually validated human blood plasma protein reference set , 2008 .

[13]  R. Beavis,et al.  A method for reducing the time required to match protein sequences with tandem mass spectra. , 2003, Rapid communications in mass spectrometry : RCM.

[14]  A. Chinnaiyan,et al.  Current affairs in quantitative targeted proteomics: multiple reaction monitoring-mass spectrometry. , 2009, Briefings in functional genomics & proteomics.

[15]  R. Aebersold,et al.  Proteomics--advances, applications and the challenges that remain. , 2002, Trends in biotechnology.

[16]  F. Regnier,et al.  Oxidative stress studies in yeast with a frataxin mutant: a proteomics perspective. , 2010, Journal of proteome research.

[17]  Antoine H P America,et al.  Comparative LC‐MS: A landscape of peaks and valleys , 2008, Proteomics.

[18]  H. Rodriguez,et al.  Reconstructing the pipeline by introducing multiplexed multiple reaction monitoring mass spectrometry for cancer biomarker verification: An NCI‐CPTC initiative perspective , 2010, Proteomics. Clinical applications.

[19]  J. Yates,et al.  A model for random sampling and estimation of relative protein abundance in shotgun proteomics. , 2004, Analytical chemistry.

[20]  Jinsam You,et al.  A simplified procedure for the reduction and alkylation of cysteine residues in proteins prior to proteolytic digestion and mass spectral analysis. , 2004, Analytical biochemistry.

[21]  Brendan MacLean,et al.  Bioinformatics Applications Note Gene Expression Skyline: an Open Source Document Editor for Creating and Analyzing Targeted Proteomics Experiments , 2022 .

[22]  Setsuo Hirohashi,et al.  Label-free Quantitative Proteomics Using Large Peptide Data Sets Generated by Nanoflow Liquid Chromatography and Mass Spectrometry* , 2006, Molecular & Cellular Proteomics.

[23]  Kristin L Cheek,et al.  Depletion of abundant plasma proteins and limitations of plasma proteomics. , 2010, Journal of proteome research.

[24]  M. Caron,et al.  Usefulness of an integrated microfluidic device (HPLC-Chip-MS) to enhance confidence in protein identification by proteomics. , 2006, Rapid communications in mass spectrometry : RCM.

[25]  Philip C. Andrews,et al.  A code and data archival and dissemination tool for the proteomics community , 2006 .

[26]  P. Hudler,et al.  Proteomic strategies and challenges in tumor metastasis research , 2010, Clinical & Experimental Metastasis.

[27]  J. Bandow.  Comparison of protein enrichment strategies for proteome analysis of plasma , 2010, Proteomics.

[28]  Amanda Paulovich,et al.  Cancer biomarkers: a systems approach , 2006, Nature Biotechnology.

[29]  Mu Wang,et al.  Searching for potential biomarkers of cisplatin resistance in human ovarian cancer using a label‐free LC/MS‐based protein quantification method , 2007, Proteomics. Clinical applications.

[30]  L. Foster,et al.  Quantitative analysis of proteome coverage and recovery rates for upstream fractionation methods in proteomics. , 2010, Journal of proteome research.

[31]  R. Bischoff,et al.  Multidimensional chromatography coupled to mass spectrometry in analysing complex proteomics samples. , 2010, Journal of separation science.

[32]  Denis Hochstrasser,et al.  Multi-dimensional HPLC/MS of the nucleolar proteome using HPLC-chip/MS. , 2006, Journal of separation science.

[33]  J. Sowers,et al.  Differential regulation of angiotensin-(1-12) in plasma and cardiac tissue in response to bilateral nephrectomy. , 2009, American journal of physiology. Heart and circulatory physiology.

[34]  Robert A. Thompson,et al.  Comparative proteomics based on stable isotope labeling and affinity selection. , 2002, Journal of mass spectrometry : JMS.

[35]  Jiri Adamec,et al.  Dynamics of protein damage in yeast frataxin mutant exposed to oxidative stress. , 2010, Omics : a journal of integrative biology.

[36]  Tommi S. Jaakkola,et al.  Maximum-likelihood estimation of optimal scaling factors for expression array normalization , 2001, SPIE BiOS.

[37]  U. Stenman,et al.  Prostate‐specific antigen forms a complex with and cleaves α1‐protease inhibitor in vitro , 1997 .

[38]  Timothy D. Veenstra,et al.  AN ACCURATE MASS TAG STRATEGY FOR QUANTITATIVE AND HIGH THROUGHPUT PROTEOME MEASUREMENTS , 2002 .

[39]  H. Yin,et al.  Microfluidic chip for peptide analysis with an integrated HPLC column, sample enrichment column, and nanoelectrospray tip. , 2005, Analytical chemistry.

[40]  S. Gygi,et al.  Quantitative analysis of complex protein mixtures using isotope-coded affinity tags , 1999, Nature Biotechnology.

[41]  Christoph H Borchers,et al.  Multi-site assessment of the precision and reproducibility of multiple reaction monitoring–based measurements of proteins in plasma , 2009, Nature Biotechnology.

[42]  Pierre Thibault,et al.  Integrated microfluidic device for mass spectrometry-based proteomics and its application to biomarker discovery programs. , 2005, Analytical chemistry.

[43]  F. Regnier,et al.  An automated method for the analysis of stable isotope labeling data in proteomics , 2005, Journal of the American Society for Mass Spectrometry.

[44]  Michael Riffle,et al.  Proteomics data repositories , 2009, Proteomics.

[45]  J. Delanghe,et al.  Hemopexin: a review of biological aspects and the role in laboratory medicine. , 2001, Clinica chimica acta; international journal of clinical chemistry.

[46]  Jing He,et al.  The Proteome Discovery Pipeline--A Data Analysis Pipeline for Mass Spectrometry-Based Differential P , 2010 .

[47]  Connie R Jimenez,et al.  Proteomics strategies for target identification and biomarker discovery in cancer. , 2009, Frontiers in bioscience.

[48]  Robert E. Kearney,et al.  A HUPO test sample study reveals common problems in mass spectrometry-based proteomics , 2009, Nature Methods.

[49]  J. Adamec,et al.  Discovery of New Biomarkers of Cancer Using Proteomics Technology , 2011 .

[50]  Jens M. Rick,et al.  Quantitative mass spectrometry in proteomics: a critical review , 2007, Analytical and bioanalytical chemistry.

[51]  Hong Zhu,et al.  Changes of lipid metabolism in plasma, liver and bile during cholesterol gallstone formation in rabbit model. , 1998, World journal of gastroenterology.

[52]  F. Regnier,et al.  Multi-dimensional liquid chromatography in proteomics--a review. , 2010, Analytica chimica acta.

[53]  F. Regnier,et al.  Signature-peptide approach to detecting proteins in complex mixtures. , 2000, Journal of chromatography. A.

[54]  Alexey I Nesvizhskii,et al.  Analysis and validation of proteomic data generated by tandem mass spectrometry , 2007, Nature Methods.

[55]  Xiang Zhang,et al.  Data pre-processing in liquid chromatography-mass spectrometry-based proteomics , 2005, Bioinform..

[56]  F. Regnier,et al.  Intrinsic subtype‐associated changes in the plasma proteome in breast cancer , 2009, Proteomics. Clinical applications.

[57]  J. Yates,et al.  An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database , 1994, Journal of the American Society for Mass Spectrometry.

[58]  P. Meleady,et al.  Proteomic approaches for serum biomarker discovery in cancer. , 2007, Anticancer research.