PMID- 25991688
OWN - NLM
STAT- MEDLINE
DCOM- 20160405
LR  - 20210217
IS  - 1535-9484 (Electronic)
IS  - 1535-9476 (Print)
IS  - 1535-9476 (Linking)
VI  - 14
IP  - 7
DP  - 2015 Jul
TI  - The Impact II, a Very High-Resolution Quadrupole Time-of-Flight Instrument (QTOF) 
      for Deep Shotgun Proteomics.
PG  - 2014-29
LID - 10.1074/mcp.M114.047407 [doi]
AB  - Hybrid quadrupole time-of-flight (QTOF) mass spectrometry is one of the two major 
      principles used in proteomics. Although based on simple fundamentals, it has over 
      the last decades greatly evolved in terms of achievable resolution, mass 
      accuracy, and dynamic range. The Bruker impact platform of QTOF instruments takes 
      advantage of these developments and here we develop and evaluate the impact II 
      for shotgun proteomics applications. Adaption of our heated liquid chromatography 
      system achieved very narrow peptide elution peaks. The impact II is equipped with 
      a new collision cell with both axial and radial ion ejection, more than doubling 
      ion extraction at high tandem MS frequencies. The new reflectron and detector 
      improve resolving power compared with the previous model up to 80%, i.e. to 
      40,000 at m/z 1222. We analyzed the ion current from the inlet capillary and 
      found very high transmission (>80%) up to the collision cell. Simulation and 
      measurement indicated 60% transfer into the flight tube. We adapted MaxQuant for 
      QTOF data, improving absolute average mass deviations to better than 1.45 ppm. 
      More than 4800 proteins can be identified in a single run of HeLa digest in a 90 
      min gradient. The workflow achieved high technical reproducibility (R2 > 0.99) 
      and accurate fold change determination in spike-in experiments in complex 
      mixtures. Using label-free quantification we rapidly quantified haploid against 
      diploid yeast and characterized overall proteome differences in mouse cell lines 
      originating from different tissues. Finally, after high pH reversed-phase 
      fractionation we identified 9515 proteins in a triplicate measurement of HeLa 
      peptide mixture and 11,257 proteins in single measurements of cerebellum-the 
      highest proteome coverage reported with a QTOF instrument so far.
CI  - (c) 2015 by The American Society for Biochemistry and Molecular Biology, Inc.
FAU - Beck, Scarlet
AU  - Beck S
AD  - From the double daggerProteomics and Signal Transduction, Max-Planck-Institute of 
      Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany;
FAU - Michalski, Annette
AU  - Michalski A
AD  -  section signBruker Daltonik GmbH, Fahrenheitstr. 4, 28359 Bremen, Germany;
FAU - Raether, Oliver
AU  - Raether O
AD  -  section signBruker Daltonik GmbH, Fahrenheitstr. 4, 28359 Bremen, Germany;
FAU - Lubeck, Markus
AU  - Lubeck M
AD  -  section signBruker Daltonik GmbH, Fahrenheitstr. 4, 28359 Bremen, Germany;
FAU - Kaspar, Stephanie
AU  - Kaspar S
AD  -  section signBruker Daltonik GmbH, Fahrenheitstr. 4, 28359 Bremen, Germany;
FAU - Goedecke, Niels
AU  - Goedecke N
AD  -  section signBruker Daltonik GmbH, Fahrenheitstr. 4, 28359 Bremen, Germany;
FAU - Baessmann, Carsten
AU  - Baessmann C
AD  -  section signBruker Daltonik GmbH, Fahrenheitstr. 4, 28359 Bremen, Germany;
FAU - Hornburg, Daniel
AU  - Hornburg D
AD  - From the double daggerProteomics and Signal Transduction, Max-Planck-Institute of 
      Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany;
FAU - Meier, Florian
AU  - Meier F
AD  - From the double daggerProteomics and Signal Transduction, Max-Planck-Institute of 
      Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany;
FAU - Paron, Igor
AU  - Paron I
AD  - From the double daggerProteomics and Signal Transduction, Max-Planck-Institute of 
      Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany;
FAU - Kulak, Nils A
AU  - Kulak NA
AD  - From the double daggerProteomics and Signal Transduction, Max-Planck-Institute of 
      Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany;
FAU - Cox, Juergen
AU  - Cox J
AD  -  paragraph signComputational Systems Biochemistry, Max-Planck-Institute of Biochemistry, Am 
      Klopferspitz 18, 82152 Martinsried, Germany.
FAU - Mann, Matthias
AU  - Mann M
AD  - From the double daggerProteomics and Signal Transduction, Max-Planck-Institute of 
      Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany; 
      mmann@biochem.mpg.de.
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20150519
PL  - United States
TA  - Mol Cell Proteomics
JT  - Molecular & cellular proteomics : MCP
JID - 101125647
RN  - 0 (Ions)
RN  - 0 (Peptides)
RN  - 0 (Proteome)
SB  - IM
MH  - Animals
MH  - Cell Line
MH  - Chromatography, Liquid
MH  - Diploidy
MH  - Haploidy
MH  - HeLa Cells
MH  - Humans
MH  - Hydrogen-Ion Concentration
MH  - Ions
MH  - Mass Spectrometry
MH  - Mice
MH  - Molecular Weight
MH  - Peptides/metabolism
MH  - Proteome/metabolism
MH  - Proteomics/*instrumentation/*methods
MH  - Reproducibility of Results
MH  - Saccharomyces cerevisiae/metabolism
MH  - Time Factors
PMC - PMC4587313
EDAT- 2015/05/21 06:00
MHDA- 2016/04/06 06:00
PMCR- 2015/05/19
CRDT- 2015/05/21 06:00
PHST- 2014/12/12 00:00 [received]
PHST- 2015/05/21 06:00 [entrez]
PHST- 2015/05/21 06:00 [pubmed]
PHST- 2016/04/06 06:00 [medline]
PHST- 2015/05/19 00:00 [pmc-release]
AID - S1535-9476(20)32864-4 [pii]
AID - M114.047407 [pii]
AID - 10.1074/mcp.M114.047407 [doi]
PST - ppublish
SO  - Mol Cell Proteomics. 2015 Jul;14(7):2014-29. doi: 10.1074/mcp.M114.047407. Epub 
      2015 May 19.