Phosphoproteome Discovery in Human Biological Fluids
Abstract
:1. Introduction
2. Bioanalytical Strategies
2.1. General Workflow Characteristics
2.2. Protein Processing
2.3. Protein Digestion
2.4. Separation of Peptide Mixtures
2.5. Phosphopeptide Enrichment
2.6. LC–MS/MS
2.7. Bioinformatics
3. Applications to Biofluid Phosphoproteome Characterization
3.1. Serum/Plasma
3.2. Urine
3.3. Cerebrospinal Fluid
3.4. Saliva
3.5. Bronchoalveolar Lavage Fluid
4. Concluding Remarks
Acknowledgments
Conflicts of Interest
Abbreviations
BAL | bronchoalveolar lavage fluid |
CID | collision-induced dissociation |
CSF | cerebrospinal fluid |
DIA | data-independent acquisition |
DDA | data-dependent acquisition |
ETD | electron-transfer dissociation |
IMAC | immobilized metal ion affinity chromatography |
iTRAQ | isobaric tag for relative and absolute quantification |
MARS | Multiple Affinity Removal System |
MDLC | multidimensional liquid chromatography |
MRM | multiple reaction monitoring |
MOAC | metal oxide affinity chromatography |
mTRAQ | mass differential tag for relative and absolute quantification |
RP | reversed-phase |
SAX | strong anion exchange |
SCX | strong cation exchange |
TMT | tandem mass tag |
TOF | time-of-flight |
UPLC | ultra-high pressure chromatography |
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Fluid Studied | Disease or Condition | Protein Depletion | MDLC | Phospho Enrichment | CID/ETD | DDA/DIA | Phosphoproteome Panel Reported | Reference |
---|---|---|---|---|---|---|---|---|
Serum | Prostate Cancer | Y | N | Y | Y/Y | DDA (qual.) | ~100 phosphopeptides | [54] |
Plasma | Normal | Y | Y | Y | Y/N | DDA (qual.) | 138 phosphopeptides/127 sites in 70 proteins | [55] |
Serum | Benign Prostate Hyperplasia | N | Y | Y | Y/N | DDA (qual.) | 375 phosphopeptides in 375 proteins | [56] |
Serum | N/A | Y | N | Y (at protein level) | Y/N | DIA (qual.) | 5800 phosphopeptides in 502 proteins | [15] |
Serum | Schizophrenia vs. Control | Y | N | Y (at protein level) | Y/N | DIA (quant.) | 59 altered phosphoproteins | [16] |
Urine | Normal | N | Y | N | Y/N | DDA (qual.) | 45 phosphopeptides/59 sites in 31 proteins | [57] |
Urine | Pregnancy (Before/after delivery) | N | N | Y | Y/N | DDA (quant.) | 130 phosphopeptides/222 sites in 105 proteins; 16 altered phosphoproteins | [17] |
Urine | Normal | N | N | Y | Y/N | DDA (qual.) | 106 phosphosites in 64 proteins | [58] |
CSF | Suspected Neurological Disorder | N | N | Y | Y/N | DDA (qual.) | 44 phosphoproteins (include 56 novel sites) | [24] |
Saliva | Normal | N | N | Y (derivatization) | Y/N | DDA (qual.) | 65 phosphoproteins | [36] |
Saliva | Normal | Y | Y | Y | Y/Y | DDA (qual.) | 217 phosphopeptides in 85 phosphoproteins | [59] |
BAL | N/A (not Lung Cancer or COPD) | Y | N | Y | Y/N | DDA (qual.) | 36 phosphopeptides/26 sites in 21 proteins | [60] |
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Giorgianni, F.; Beranova-Giorgianni, S. Phosphoproteome Discovery in Human Biological Fluids. Proteomes 2016, 4, 37. https://doi.org/10.3390/proteomes4040037
Giorgianni F, Beranova-Giorgianni S. Phosphoproteome Discovery in Human Biological Fluids. Proteomes. 2016; 4(4):37. https://doi.org/10.3390/proteomes4040037
Chicago/Turabian StyleGiorgianni, Francesco, and Sarka Beranova-Giorgianni. 2016. "Phosphoproteome Discovery in Human Biological Fluids" Proteomes 4, no. 4: 37. https://doi.org/10.3390/proteomes4040037