Literature DB >> 28691345

The Skyline ecosystem: Informatics for quantitative mass spectrometry proteomics.

Lindsay K Pino1, Brian C Searle1, James G Bollinger1, Brook Nunn1, Brendan MacLean1, Michael J MacCoss1.   

Abstract

Skyline is a freely available, open-source Windows client application for accelerating targeted proteomics experimentation, with an emphasis on the proteomics and mass spectrometry community as users and as contributors. This review covers the informatics encompassed by the Skyline ecosystem, from computationally assisted targeted mass spectrometry method development, to raw acquisition file data processing, and quantitative analysis and results sharing.
© 2017 Wiley Periodicals, Inc.

Entities:  

Keywords:  informatics; quantitative mass spectrometry; targeted proteomics

Mesh：

Substances：

Year:  2017        PMID： 28691345      PMCID： PMC5799042          DOI： 10.1002/mas.21540

Source DB:  PubMed          Journal:  Mass Spectrom Rev        ISSN： 0277-7037            Impact factor:   10.946


  90 in total

1.  Automated approach for quantitative analysis of complex peptide mixtures from tandem mass spectra.

Authors:  John D Venable; Meng-Qiu Dong; James Wohlschlegel; Andrew Dillin; John R Yates
Journal:  Nat Methods       Date:  2004-09-29       Impact factor: 28.547

2.  Sequence-specific retention calculator. A family of peptide retention time prediction algorithms in reversed-phase HPLC: applicability to various chromatographic conditions and columns.

Authors:  Vic Spicer; Andriy Yamchuk; John Cortens; Sandra Sousa; Werner Ens; Kenneth G Standing; John A Wilkins; Oleg V Krokhin
Journal:  Anal Chem       Date:  2007-10-16       Impact factor: 6.986

3.  Using Data Independent Acquisition (DIA) to Model High-responding Peptides for Targeted Proteomics Experiments.

Authors:  Brian C Searle; Jarrett D Egertson; James G Bollinger; Andrew B Stergachis; Michael J MacCoss
Journal:  Mol Cell Proteomics       Date:  2015-06-22       Impact factor: 5.911

Review 4.  Trans-Proteomic Pipeline, a standardized data processing pipeline for large-scale reproducible proteomics informatics.

Authors:  Eric W Deutsch; Luis Mendoza; David Shteynberg; Joseph Slagel; Zhi Sun; Robert L Moritz
Journal:  Proteomics Clin Appl       Date:  2015-04-02       Impact factor: 3.494

5.  A framework for installable external tools in Skyline.

Authors:  Daniel Broudy; Trevor Killeen; Meena Choi; Nicholas Shulman; Deepak R Mani; Susan E Abbatiello; Deepak Mani; Rushdy Ahmad; Alexandria K Sahu; Birgit Schilling; Kaipo Tamura; Yuval Boss; Vagisha Sharma; Bradford W Gibson; Steven A Carr; Olga Vitek; Michael J MacCoss; Brendan MacLean
Journal:  Bioinformatics       Date:  2014-05-09       Impact factor: 6.937

6.  Correlation between y-type ions observed in ion trap and triple quadrupole mass spectrometers.

Authors:  Carly A Sherwood; Ashley Eastham; Lik Wee Lee; Jenni Risler; Olga Vitek; Daniel B Martin
Journal:  J Proteome Res       Date:  2009-09       Impact factor: 4.466

7.  Ranking Fragment Ions Based on Outlier Detection for Improved Label-Free Quantification in Data-Independent Acquisition LC-MS/MS.

Authors:  Aivett Bilbao; Ying Zhang; Emmanuel Varesio; Jeremy Luban; Caterina Strambio-De-Castillia; Frédérique Lisacek; Gérard Hopfgartner
Journal:  J Proteome Res       Date:  2015-10-14       Impact factor: 4.466

8.  PEAKS DB: de novo sequencing assisted database search for sensitive and accurate peptide identification.

Authors:  Jing Zhang; Lei Xin; Baozhen Shan; Weiwu Chen; Mingjie Xie; Denis Yuen; Weiming Zhang; Zefeng Zhang; Gilles A Lajoie; Bin Ma
Journal:  Mol Cell Proteomics       Date:  2011-12-20       Impact factor: 5.911

Review 9.  Comparing protein abundance and mRNA expression levels on a genomic scale.

Authors:  Dov Greenbaum; Christopher Colangelo; Kenneth Williams; Mark Gerstein
Journal:  Genome Biol       Date:  2003-08-29       Impact factor: 13.583

10.  PRIDE: new developments and new datasets.

Authors:  Philip Jones; Richard G Côté; Sang Yun Cho; Sebastian Klie; Lennart Martens; Antony F Quinn; David Thorneycroft; Henning Hermjakob
Journal:  Nucleic Acids Res       Date:  2007-11-22       Impact factor: 16.971
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  127 in total

1.  Skyline for Small Molecules: A Unifying Software Package for Quantitative Metabolomics.

Authors:  Kendra J Adams; Brian Pratt; Neelanjan Bose; Laura G Dubois; Lisa St John-Williams; Kevin M Perrott; Karina Ky; Pankaj Kapahi; Vagisha Sharma; Michael J MacCoss; M Arthur Moseley; Carol A Colton; Brendan X MacLean; Birgit Schilling; J Will Thompson
Journal:  J Proteome Res       Date:  2020-03-26       Impact factor: 4.466

2.  Quantification of Inflammasome Adaptor Protein ASC in Biological Samples by Multiple-Reaction Monitoring Mass Spectrometry.

Authors:  Annegret Ulke-Lemée; Arthur Lau; Michelle C Nelson; Matthew T James; Daniel A Muruve; Justin A MacDonald
Journal:  Inflammation       Date:  2018-08       Impact factor: 4.092

3.  Rapid Assessment of Contaminants and Interferences in Mass Spectrometry Data Using Skyline.

Authors:  Matthew J Rardin
Journal:  J Am Soc Mass Spectrom       Date:  2018-04-17       Impact factor: 3.109

4.  Proteome-wide Interrogation of Small GTPases Regulated by N6-Methyladenosine Modulators.

Authors:  Yen-Yu Yang; Kailin Yu; Lin Li; Ming Huang; Yinsheng Wang
Journal:  Anal Chem       Date:  2020-07-07       Impact factor: 6.986

5.  An Internal Standard for Assessing Phosphopeptide Recovery from Metal Ion/Oxide Enrichment Strategies.

Authors:  Joao A Paulo; Jose Navarrete-Perea; Alison R Erickson; Jeffrey Knott; Steven P Gygi
Journal:  J Am Soc Mass Spectrom       Date:  2018-04-18       Impact factor: 3.109

Review 6.  Clinical potential of mass spectrometry-based proteogenomics.

Authors:  Bing Zhang; Jeffrey R Whiteaker; Andrew N Hoofnagle; Geoffrey S Baird; Karin D Rodland; Amanda G Paulovich
Journal:  Nat Rev Clin Oncol       Date:  2019-04       Impact factor: 66.675

7.  TKO6: A Peptide Standard To Assess Interference for Unit-Resolved Isobaric Labeling Platforms.

Authors:  Joao A Paulo; Jose Navarrete-Perea; Sanjukta Guha Thakurta; Steven P Gygi
Journal:  J Proteome Res       Date:  2018-12-06       Impact factor: 4.466

8.  Highly Multiplex Targeted Proteomics Enabled by Real-Time Chromatographic Alignment.

Authors:  Philip M Remes; Ping Yip; Michael J MacCoss
Journal:  Anal Chem       Date:  2020-08-12       Impact factor: 6.986

9.  A quantitative thiol reactivity profiling platform to analyze redox and electrophile reactive cysteine proteomes.

Authors:  Ling Fu; Zongmin Li; Keke Liu; Caiping Tian; Jixiang He; Jingyang He; Fuchu He; Ping Xu; Jing Yang
Journal:  Nat Protoc       Date:  2020-07-20       Impact factor: 13.491

10.  Cumulative deamidations of the major lens protein γS-crystallin increase its aggregation during unfolding and oxidation.

Authors:  Calvin J Vetter; David C Thorn; Samuel G Wheeler; Charlie C Mundorff; Kate A Halverson; Thomas E Wales; Ujwal P Shinde; John R Engen; Larry L David; John A Carver; Kirsten J Lampi
Journal:  Protein Sci       Date:  2020-09       Impact factor: 6.725
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