Literature DB >> 22593248

The spectra count label-free quantitation in cancer proteomics.

Weidong Zhou1, Lance A Liotta, Emanuel F Petricoin.   

Abstract

Mass spectrometry is used routinely for large-scale protein identification from complex biological mixtures. Recently, relative quantitation approach on the basis of spectra count has been applied in several cancer proteomic studies. In this review, we examine the mechanism of this technique and highlight several important parameters associated with its application.

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Year:  2012        PMID: 22593248      PMCID: PMC3761408     

Source DB:  PubMed          Journal:  Cancer Genomics Proteomics        ISSN: 1109-6535            Impact factor:   4.069


  42 in total

1.  Exponentially modified protein abundance index (emPAI) for estimation of absolute protein amount in proteomics by the number of sequenced peptides per protein.

Authors:  Yasushi Ishihama; Yoshiya Oda; Tsuyoshi Tabata; Toshitaka Sato; Takeshi Nagasu; Juri Rappsilber; Matthias Mann
Journal:  Mol Cell Proteomics       Date:  2005-06-14       Impact factor: 5.911

2.  An evaluation, comparison, and accurate benchmarking of several publicly available MS/MS search algorithms: sensitivity and specificity analysis.

Authors:  Eugene A Kapp; Frédéric Schütz; Lisa M Connolly; John A Chakel; Jose E Meza; Christine A Miller; David Fenyo; Jimmy K Eng; Joshua N Adkins; Gilbert S Omenn; Richard J Simpson
Journal:  Proteomics       Date:  2005-08       Impact factor: 3.984

3.  Comparative evaluation of mass spectrometry platforms used in large-scale proteomics investigations.

Authors:  Joshua E Elias; Wilhelm Haas; Brendan K Faherty; Steven P Gygi
Journal:  Nat Methods       Date:  2005-09       Impact factor: 28.547

Review 4.  Mass spectrometry and protein analysis.

Authors:  Bruno Domon; Ruedi Aebersold
Journal:  Science       Date:  2006-04-14       Impact factor: 47.728

Review 5.  Analyzing chromatin remodeling complexes using shotgun proteomics and normalized spectral abundance factors.

Authors:  Laurence Florens; Michael J Carozza; Selene K Swanson; Marjorie Fournier; Michael K Coleman; Jerry L Workman; Michael P Washburn
Journal:  Methods       Date:  2006-12       Impact factor: 3.608

6.  A top-down/bottom-up study of the ribosomal proteins of Caulobacter crescentus.

Authors:  William E Running; Shobha Ravipaty; Jonathan A Karty; James P Reilly
Journal:  J Proteome Res       Date:  2007-01       Impact factor: 4.466

7.  Proteomics of mouse BRCA1-deficient mammary tumors identifies DNA repair proteins with potential diagnostic and prognostic value in human breast cancer.

Authors:  Marc Warmoes; Janneke E Jaspers; Thang V Pham; Sander R Piersma; Gideon Oudgenoeg; Maarten P G Massink; Quinten Waisfisz; Sven Rottenberg; Epie Boven; Jos Jonkers; Connie R Jimenez
Journal:  Mol Cell Proteomics       Date:  2012-02-24       Impact factor: 5.911

8.  Direct analysis of protein complexes using mass spectrometry.

Authors:  A J Link; J Eng; D M Schieltz; E Carmack; G J Mize; D R Morris; B M Garvik; J R Yates
Journal:  Nat Biotechnol       Date:  1999-07       Impact factor: 54.908

9.  Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents.

Authors:  Philip L Ross; Yulin N Huang; Jason N Marchese; Brian Williamson; Kenneth Parker; Stephen Hattan; Nikita Khainovski; Sasi Pillai; Subhakar Dey; Scott Daniels; Subhasish Purkayastha; Peter Juhasz; Stephen Martin; Michael Bartlet-Jones; Feng He; Allan Jacobson; Darryl J Pappin
Journal:  Mol Cell Proteomics       Date:  2004-09-22       Impact factor: 5.911

10.  Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry.

Authors:  An Chi; Curtis Huttenhower; Lewis Y Geer; Joshua J Coon; John E P Syka; Dina L Bai; Jeffrey Shabanowitz; Daniel J Burke; Olga G Troyanskaya; Donald F Hunt
Journal:  Proc Natl Acad Sci U S A       Date:  2007-02-07       Impact factor: 11.205

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  13 in total

1.  Proteomic Interrogation in Cancer Biomarker.

Authors:  Un-Beom Kang
Journal:  Adv Exp Med Biol       Date:  2021       Impact factor: 2.622

2.  Capturing and identification of differentially expressed fucome by a gel free and label free approach.

Authors:  Chanida Puangpila; Ziad El Rassi
Journal:  J Chromatogr B Analyt Technol Biomed Life Sci       Date:  2015-03-14       Impact factor: 3.205

3.  An Integrated Workflow for Global, Glyco-, and Phospho-proteomic Analysis of Tumor Tissues.

Authors:  Yangying Zhou; Tung-Shing Mamie Lih; Ganglong Yang; Shao-Yung Chen; Lijun Chen; Daniel W Chan; Hui Zhang; Qing Kay Li
Journal:  Anal Chem       Date:  2020-01-03       Impact factor: 6.986

Review 4.  Recent advances in mass spectrometry analysis of neuropeptides.

Authors:  Ashley Phetsanthad; Nhu Q Vu; Qing Yu; Amanda R Buchberger; Zhengwei Chen; Caitlin Keller; Lingjun Li
Journal:  Mass Spectrom Rev       Date:  2021-09-24       Impact factor: 9.011

5.  Efficient Microscale Basic Reverse Phase Peptide Fractionation for Global and Targeted Proteomics.

Authors:  Hyoung-Joo Lee; Hye-Jung Kim; Daniel C Liebler
Journal:  J Proteome Res       Date:  2016-06-13       Impact factor: 4.466

6.  Predicting clinical response to anticancer drugs using an ex vivo platform that captures tumour heterogeneity.

Authors:  Biswanath Majumder; Ulaganathan Baraneedharan; Saravanan Thiyagarajan; Padhma Radhakrishnan; Harikrishna Narasimhan; Muthu Dhandapani; Nilesh Brijwani; Dency D Pinto; Arun Prasath; Basavaraja U Shanthappa; Allen Thayakumar; Rajagopalan Surendran; Govind K Babu; Ashok M Shenoy; Moni A Kuriakose; Guillaume Bergthold; Peleg Horowitz; Massimo Loda; Rameen Beroukhim; Shivani Agarwal; Shiladitya Sengupta; Mallikarjun Sundaram; Pradip K Majumder
Journal:  Nat Commun       Date:  2015-02-27       Impact factor: 14.919

7.  LC-MS/MS Analysis Unravels Deep Oxidation of Manganese Superoxide Dismutase in Kidney Cancer.

Authors:  Zuohui Zhao; Kazem M Azadzoi; Han-Pil Choi; Ruirui Jing; Xin Lu; Cuiling Li; Fengqin Wang; Jiaju Lu; Jing-Hua Yang
Journal:  Int J Mol Sci       Date:  2017-02-04       Impact factor: 5.923

8.  Application of clinical proteomics in acute respiratory distress syndrome.

Authors:  Maneesh Bhargava; LeeAnn Higgins; Christine H Wendt; David H Ingbar
Journal:  Clin Transl Med       Date:  2014-10-15

9.  MetaPro-IQ: a universal metaproteomic approach to studying human and mouse gut microbiota.

Authors:  Xu Zhang; Zhibin Ning; Janice Mayne; Jasmine I Moore; Jennifer Li; James Butcher; Shelley Ann Deeke; Rui Chen; Cheng-Kang Chiang; Ming Wen; David Mack; Alain Stintzi; Daniel Figeys
Journal:  Microbiome       Date:  2016-06-24       Impact factor: 14.650

10.  Quantification of species-specific meat proteins in cooked and smoked sausages using infusion mass spectrometry.

Authors:  Magdalena Montowska; Anita Spychaj
Journal:  J Food Sci Technol       Date:  2018-09-28       Impact factor: 2.701

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