NDLI: Advancing cell biology through proteomics in space and time (PROSPECTS).

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A Protein Epitope Signature Tag (PrEST) library allows SILAC-based absolute quantification and multiplexed determination of protein copy numbers in cell lines.

Systematic analysis of protein pools, isoforms, and modifications affecting turnover and subcellular localization.

System-wide perturbation analysis with nearly complete coverage of the yeast proteome by single-shot ultra HPLC runs on a bench top Orbitrap.

Characterization of MRFAP1 turnover and interactions downstream of the NEDD8 pathway.

Antibody-based protein profiling of the human chromosome 21.

Estimation of absolute protein quantities of unlabeled samples by selected reaction monitoring mass spectrometry.

Ultra high resolution linear ion trap Orbitrap mass spectrometer (Orbitrap Elite) facilitates top down LC MS/MS and versatile peptide fragmentation modes.

Quantitative proteomics reveals that Hsp90 inhibition preferentially targets kinases and the DNA damage response.

A framework for intelligent data acquisition and real-time database searching for shotgun proteomics.

Joining forces: integrating proteomics and cross-linking with the mass spectrometry of intact complexes.

Kinetics in signal transduction pathways involving promiscuous oligomerizing receptors can be determined by receptor specificity: apoptosis induction by TRAIL.

Comparative proteomic analysis of eleven common cell lines reveals ubiquitous but varying expression of most proteins.

Expanding the chemical cross-linking toolbox by the use of multiple proteases and enrichment by size exclusion chromatography.

Analysis of high accuracy, quantitative proteomics data in the MaxQB database.

Advancing cell biology through proteomics in space and time (PROSPECTS).

Identification of autophagosome-associated proteins and regulators by quantitative proteomic analysis and genetic screens.

Year: 2012 Volume: 11 Issue: 2

Year: 2012 Volume: 11 Issue: 1

Year: 2011 Volume: 10

Advancing cell biology through proteomics in space and time (PROSPECTS).

Content Provider	World Health Organization (WHO)-Global Index Medicus
Author	Lamond, Angus I. Uhlen, Mathias Horning, Stevan Makarov, Alexander Robinson, Carol V. Serrano, Luis Hartl, F. Ulrich Baumeister, Wolfgang Werenskiold, Anne Katrin Andersen, Jens S. Vorm, Ole Linial, Michal Aebersold, Ruedi Mann, Matthias
Description	Author Affiliation: Lamond AI ( Centre for Gene Regulation & Expression, College of Life Sciences, University of Dundee, Dundee DD1 5EH United Kingdom. a.i.lamond@dundee.ac.uk)
Abstract	The term 'proteomics' encompasses the large-scale detection and analysis of proteins and their post-translational modifications. Driven by major improvements in mass spectrometric instrumentation, methodology, and data analysis, the proteomics field has burgeoned in recent years. It now provides a range of sensitive and quantitative approaches for measuring protein structures and dynamics that promise to revolutionize our understanding of cell biology and molecular mechanisms in both human cells and model organisms. The Proteomics Specification in Time and Space (PROSPECTS) Network is a unique EU-funded project that brings together leading European research groups, spanning from instrumentation to biomedicine, in a collaborative five year initiative to develop new methods and applications for the functional analysis of cellular proteins. This special issue of Molecular and Cellular Proteomics presents 16 research papers reporting major recent progress by the PROSPECTS groups, including improvements to the resolution and sensitivity of the Orbitrap family of mass spectrometers, systematic detection of proteins using highly characterized antibody collections, and new methods for absolute as well as relative quantification of protein levels. Manuscripts in this issue exemplify approaches for performing quantitative measurements of cell proteomes and for studying their dynamic responses to perturbation, both during normal cellular responses and in disease mechanisms. Here we present a perspective on how the proteomics field is moving beyond simply identifying proteins with high sensitivity toward providing a powerful and versatile set of assay systems for characterizing proteome dynamics and thereby creating a new 'third generation' proteomics strategy that offers an indispensible tool for cell biology and molecular medicine.
File Format	HTM / HTML
ISSN	15359476
e-ISSN	15359484
DOI	10.1074/mcp.O112.017731
Journal	Molecular & Cellular Proteomics
Issue Number	3
Volume Number	11
Language	English
Publisher	American Society for Biochemistry and Molecular Biology
Publisher Date	2012-03-01
Publisher Place	United States
Access Restriction	Open
Subject Keyword	Discipline Proteomics Cell Biology Mass Spectrometry Proteome Metabolism Proteomics Protein Processing, Post-translational Time Factors Research Support, Non-u.s. Gov't
Content Type	Text
Resource Type	Article
Subject	Medicine Analytical Chemistry Molecular Biology Biochemistry

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

Fast multi-blind modification search through tandem mass spectrometry.

The Expanding Landscape of the Thiol Redox Proteome.

Proteomics beyond trypsin.

MASH Suite Pro: A Comprehensive Software Tool for Top-Down Proteomics.

Transferred subgroup false discovery rate for rare post-translational modifications detected by mass spectrometry.

Mass spectrometry: reconnaissance at the Frontiers of biology.

Modification site localization scoring: strategies and performance.

Proteolytic post-translational modification of proteins: proteomic tools and methodology.

Discovery of O-GlcNAc-modified proteins in published large-scale proteome data.

Advancing cell biology through proteomics in space and time (PROSPECTS).

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The Expanding Landscape of the Thiol Redox Proteome.

Proteomics beyond trypsin.

MASH Suite Pro: A Comprehensive Software Tool for Top-Down Proteomics.

Transferred subgroup false discovery rate for rare post-translational modifications detected by mass spectrometry.

Mass spectrometry: reconnaissance at the Frontiers of biology.

Modification site localization scoring: strategies and performance.

Proteolytic post-translational modification of proteins: proteomic tools and methodology.

Discovery of O-GlcNAc-modified proteins in published large-scale proteome data.

Advancing cell biology through proteomics in space and time (PROSPECTS).