Parallel Reaction Monitoring for High Resolution and High Mass Accuracy Quantitative, Targeted Proteomics

While the number and identity of proteins expressed in a single human cell type is currently unknown, this fundamental question can be addressed by advanced mass spectrometry (MS)-based proteomics. Online liquid chromatography coupled to high-resolution MS and MS/MS yielded 166 420 peptides with unique amino-acid sequence from HeLa cells. These peptides identified 10 255 different human proteins encoded by 9207 human genes, providing a lower limit on the proteome in this cancer cell line. Deep transcriptome sequencing revealed transcripts for nearly all detected proteins. We calculate copy numbers for the expressed proteins and show that the abundances of >90% of them are within a factor 60 of the median protein expression level. Comparisons of the proteome and the transcriptome, and analysis of protein complex databases and GO categories, suggest that we achieved deep coverage of the functional transcriptome and the proteome of a single cell type.

/pdf/deep-proteome-and-transcriptome-mapping-of-a-human-cancer-2jn3nrfyy7.pdf

Deep proteome and transcriptome mapping of a human cancer cell line

A Proteome-wide, Quantitative Survey of In Vivo Ubiquitylation Sites Reveals Widespread Regulatory Roles

https://www.bumc.bu.edu/msr/files/2013/02/mann.pdf

Precision Mapping of an In Vivo N-Glycoproteome Reveals Rigid Topological and Sequence Constraints

http://www.mass-spec.espci.fr/sites/www.mass-spec.espci.fr/IMG/pdf/QExactive_MMann.pdf

Mass Spectrometry-based Proteomics Using Q Exactive, a High-performance Benchtop Quadrupole Orbitrap Mass Spectrometer

A Dual Pressure Linear Ion Trap Orbitrap Instrument with Very High Sequencing Speed

An improved method of mass analyzing a sample in a three-dimensional quadruple ion trap with varying fields is disclosed. The dynamic range and sensitivity of previous methods is increased by controlling the number of sample ions formed in the ion trap to avoid saturation and space charge.

Method of increasing the dynamic range and sensitivity of a quadrupole ion trap mass spectrometer

There is described a method of generating product ions in a quadrupole ion trap in which the amplitude of the applied excitation voltage for an ion of a given mass-to-charge ratio (m/z) is linearly related to its mass-to-charge ratio (m/z).

Method of ion fragmentation in a quadrupole ion trap

There is provided a quadrupole ion trap mass spectrometer of the type having a plurality of ring electrodes and defining a trapping volume (19). The quadrupole potential faults arising from apertures in the electrodes are corrected by an apertured shim electrode (41, 42) placed within and spaced from the walls of the electrode apertures (16, 18).

Quadrupole ion trap with electronic shims

A chromium or oxidized chromium surface for use in sample analyzing and ionizing apparatus, such as an ion trap or ionization chamber, which does not degrade or decompose a sample in contact with the surface.

Dennis M. Taylor

Papers

A Dual Pressure Linear Ion Trap Orbitrap Instrument with Very High Sequencing Speed

Method of increasing the dynamic range and sensitivity of a quadrupole ion trap mass spectrometer

Method of ion fragmentation in a quadrupole ion trap

Quadrupole ion trap with electronic shims

Metal surfaces for sample analyzing and ionizing apparatus