Developments in quantitative mass spectrometry for the analysis of proteome dynamics

Hughes, Christopher J.; Krijgsveld, Jeroen

doi:10.1016/j.tibtech.2012.09.007

Cited by 19 publications

(19 citation statements)

References 76 publications

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“…Transcriptome and proteome dynamics [37,52,86]: Pulse-chase labeling methodologies for RNA (e.g. 4-thiouracil) or protein (e.g.…”

Section: Rna-imagingmentioning

confidence: 99%

“…Extending this type of information to the hundreds of other RBPs will no doubt uncover other such stoichiometric relationships, which can be accomplished by UV-crosslinking coupled to quantitative mass spectrometry (MS) analysis of RNApeptide pairs. Quantitative MS remains a challenge, but recent advances are providing the tools necessary to tackle these types of questions [37,38], such that the rules governing RNP composition may be better defined in the near future. …”

mentioning

confidence: 99%

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Emerging properties of nuclear RNP biogenesis and export

Oeffinger¹,

Montpetit²

2015

Current Opinion in Cell Biology

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“…Transcriptome and proteome dynamics [37,52,86]: Pulse-chase labeling methodologies for RNA (e.g. 4-thiouracil) or protein (e.g.…”

Section: Rna-imagingmentioning

confidence: 99%

mentioning

confidence: 99%

Emerging properties of nuclear RNP biogenesis and export

Oeffinger¹,

Montpetit²

2015

Current Opinion in Cell Biology

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“…However, although genomic tools can provide great insights in such quests, the execution of the genetic plan is carried out for a large part by the proteins activities [17] and that is why many proteomics studies in the last decade have aimed at elucidating the host-parasite interactions. The use of proteomics has been promoted by the development of new user-friendly tools such as free gel approaches [18], [19]. Quantitative metabolic labelling techniques such as SILAC (Stable Isotope Labelling by Amino acids in Cell culture) have frequently been coupled to Mass Spectrometry (MS) for acquisition of quantitative data on changes in protein abundance between cells or experimental conditions [18].…”

Section: Introductionmentioning

confidence: 99%

Hijacking of Host Cellular Functions by an Intracellular Parasite, the Microsporidian Anncaliia algerae

et al. 2014

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Intracellular pathogens including bacteria, viruses and protozoa hijack host cell functions to access nutrients and to bypass cellular defenses and immune responses. These strategies have been acquired through selective pressure and allowed pathogens to reach an appropriate cellular niche for their survival and growth. To get new insights on how parasites hijack host cellular functions, we developed a SILAC (Stable Isotope Labeling by Amino Acids in Cell culture) quantitative proteomics workflow. Our study focused on deciphering the cross-talk in a host-parasite association, involving human foreskin fibroblasts (HFF) and the microsporidia Anncaliia algerae, a fungus related parasite with an obligate intracellular lifestyle and a strong host dependency. The host-parasite cross-talk was analyzed at five post-infection times 1, 6, 12 and 24 hours post-infection (hpi) and 8 days post-infection (dpi). A significant up-regulation of four interferon-induced proteins with tetratricopeptide repeats IFIT1, IFIT2, IFIT3 and MX1 was observed at 8 dpi suggesting a type 1 interferon (IFN) host response. Quantitative alteration of host proteins involved in biological functions such as signaling (STAT1, Ras) and reduction of the translation activity (EIF3) confirmed a host type 1 IFN response. Interestingly, the SILAC approach also allowed the detection of 148 A. algerae proteins during the kinetics of infection. Among these proteins many are involved in parasite proliferation, and an over-representation of putative secreted effectors proteins was observed. Finally our survey also suggests that A. algerae could use a transposable element as a lure strategy to escape the host innate immune system.

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“…[1] Precursor isotopic labeling uses light and heavy (e.g., 2 H, 13 C, 15 N, 18 O) chemical tags to derivatize two or three protein samples that are pooled into a single mixture. In the precursor MS scan, pairs or triplets of peptide peaks are detected.…”

mentioning

confidence: 99%

“…In the precursor MS scan, pairs or triplets of peptide peaks are detected. [2,3] Such methods include stable isotope labeling by amino acids in cell culture (SILAC), [4] acetylation, [5] dimethylation, [6] isotope-coded affinity tags (ICAT), [7] 16 O/ 18 O labeling, [8] isotope coded protein labeling, [9] and neutron encoded labeling. [10] A second approach uses isobaric tags such as tandem mass tags (TMT), [11] isobaric tags for relative and absolute quantitation (iTRAQ), [12] deuterium isobaric amine-reactive tags (DiART), [13] and dimethyl leucine tags.…”

mentioning

confidence: 99%