The plasma peptides of sepsis
AbstractBackgroundA practical strategy to discover sepsis specific proteins may be to compare the plasma peptides and proteins from patients in the intensive care unit with and without sepsis. The aim was to discover proteins and/or peptides that show greater observation frequency and/or precursor intensity in sepsis. The endogenous tryptic peptides of ICU-Sepsis were compared to ICU Control, ovarian cancer, breast cancer, female normal, sepsis, heart attack, Alzheimer ’s and multiple sclerosis along with their institution-matched controls, female normals and normal samples collected directly onto ice.MethodsEndogeno...
Source: Clinical Proteomics - July 2, 2020 Category: Biochemistry Source Type: research

Identification of pathogens from native urine samples by MALDI-TOF/TOF tandem mass spectrometry
ConclusionsOur findings indicate that mass spectrometry has great potential as a reliable high-throughput tool for microbial pathogen identification in human urine samples. In this case, the MALDI-TOF/TOF, was used as an analytical tool for the determination of bacteria in urine samples, and the results obtained emphasize high importance of storage conditions and sample preparation method impacting reliability of MS2 data analysis. The proposed method is simple enough to be utilized in existing clinical settings and is highly suitable for suspected single organism infectious etiologies. Further research is required in orde...
Source: Clinical Proteomics - June 23, 2020 Category: Biochemistry Source Type: research

Laser capture microdissection coupled mass spectrometry (LCM-MS) for spatially resolved analysis of formalin-fixed and stained human lung tissues
ConclusionHerein we show that our multistep sample preparation methodology of LCM-MS can identify distinct, characteristic proteomic compositions of anatomical features within complex fixed and stained tissues. (Source: Clinical Proteomics)
Source: Clinical Proteomics - June 17, 2020 Category: Biochemistry Source Type: research

Activity-based protein profiling guided identification of urine proteinase 3 activity in subclinical rejection after renal transplantation
ConclusionsThere appear to be limited qualitative and quantitative differences in serine hydrolase activity in patients with subclinical versus clinical renal transplant rejection. The majority of enzymes identified were present in samples from both groups implying that in-gel quantitative differences may largely relate to the activity status of shared enzymes. However qualitative compositional differences were also observed indicating differential activities. The PR3/PRTN3 analyses indicate that the activity status of urine in transplant patients is dynamic possibly reflecting changes in the underlying processes in the tr...
Source: Clinical Proteomics - June 16, 2020 Category: Biochemistry Source Type: research

Human follicular fluid proteome reveals association between overweight status and oocyte maturation abnormality
ConclusionsOur work provided a new complementary high-confidence HFF dataset involved in oocyte maturation, and these altered HFF proteins might have clinical relevance and diagnostic and prognostic value for abnormal oocyte maturation in overweight status women. (Source: Clinical Proteomics)
Source: Clinical Proteomics - June 8, 2020 Category: Biochemistry Source Type: research

A comprehensive systematic review of CSF proteins and peptides that define Alzheimer ’s disease
ConclusionsOur study reveals a panel of 27 proteins and 21 peptides highly altered in AD with consistent statistical significance; this panel constitutes a potent tool for the classification and diagnosis of AD. (Source: Clinical Proteomics)
Source: Clinical Proteomics - June 5, 2020 Category: Biochemistry Source Type: research

Proteomic analysis of human synovial fluid reveals potential diagnostic biomarkers for ankylosing spondylitis
ConclusionWe performed quantitative comparative proteomic analysis using by LC –MS/MS of the SF from four disease states: RA, gout, and OA. This systematic comparison revealed novel differentially expressed proteins in AS SF, as well as two previously reported candidate biomarkers. We further verified the expression of MMP3, C9 and CFHR5 by western blot. These proteins may s erve as diagnostic or prognostic biomarkers in patients with AS, and may thus improve the clinical outcomes of this serious disease. (Source: Clinical Proteomics)
Source: Clinical Proteomics - June 1, 2020 Category: Biochemistry Source Type: research

Targeted mass spectrometry to quantify brain-derived cerebrospinal fluid biomarkers in Alzheimer ’s disease
ConclusionCollectively these findings highlight the utility of targeted MS approaches to quantify biomarkers associated with AD that could be used for monitoring disease progression, stratifying patients for clinical trials and measuring therapeutic response. (Source: Clinical Proteomics)
Source: Clinical Proteomics - May 29, 2020 Category: Biochemistry Source Type: research

New risk score for predicting steroid resistance in patients with focal segmental glomerulosclerosis or minimal change disease
ConclusionsOur study identified a 3-variable risk score in predicting steroid resistance in patients with FSGS or MCD. (Source: Clinical Proteomics)
Source: Clinical Proteomics - May 29, 2020 Category: Biochemistry Source Type: research

Identification of TUBB2A by quantitative proteomic analysis as a novel biomarker for the prediction of distant metastatic breast cancer
ConclusionsOur report is the first study to examine the distant metastatic breast cancer proteome using FFPE tissues. The depth of our dataset allowed us to discover a novel biomarker candidate and a proteomic characteristics of distant metastatic breast cancer. Distinct molecular features of various breast cancer subtypes were also established. Our proteomic data constitute a valuable resource for research on distant metastatic breast cancer. (Source: Clinical Proteomics)
Source: Clinical Proteomics - May 24, 2020 Category: Biochemistry Source Type: research

Effects of cryopreservation and long-term culture on biological characteristics and proteomic profiles of human umbilical cord-derived mesenchymal stem cells
ConclusionThis suggests that protein expression may be used as an indicator of hUC-MSCs security testing before applying in clinical settings, and it is also expected to provide the foundation or standardization guide of hUC-MSCs applications in regenerative medicine. (Source: Clinical Proteomics)
Source: Clinical Proteomics - May 24, 2020 Category: Biochemistry Source Type: research

Recent advances in mass spectrometry based clinical proteomics: applications to cancer research
AbstractCancer biomarkers have transformed current practices in the oncology clinic. Continued discovery and validation are crucial for improving early diagnosis, risk stratification, and monitoring patient response to treatment. Profiling of the tumour genome and transcriptome are now established tools for the discovery of novel biomarkers, but alterations in proteome expression are more likely to reflect changes in tumour pathophysiology. In the past, clinical diagnostics have strongly relied on antibody-based detection strategies, but these methods carry certain limitations. Mass spectrometry (MS) is a powerful method t...
Source: Clinical Proteomics - May 24, 2020 Category: Biochemistry Source Type: research

Mass spectrometry-based microbiological testing for blood stream infection
ConclusionMALDI-TOF MS is now an essential tool for rapid bacterial ID of pathogens that cause blood stream infection. For the purpose of assessment of susceptibility and resistance to antibiotics of the pathogens, the roles of liquid chromatography (LC) coupled with tandem mass spectrometry (MS/MS) will increase in the future. (Source: Clinical Proteomics)
Source: Clinical Proteomics - May 13, 2020 Category: Biochemistry Source Type: research

Development of a novel method for the quantification of tyrosine 39 phosphorylated α- and β-synuclein in human cerebrospinal fluid
ConclusionsWe anticipate that this optimized two-step enrichment-based PRM detection method will help monitor c-Abl activation in PD patients and can also be used to quantify other phosphotyrosine peptides of low abundance in biological samples. (Source: Clinical Proteomics)
Source: Clinical Proteomics - May 4, 2020 Category: Biochemistry Source Type: research

A comprehensive analysis of sialolith proteins and the clinical implications
ConclusionSialolith formation presents similarities with the hyperoxaluria that forms kidney stones, which suggests the possibility of a common origin. Further verification of a common origin could fundamentally change the way in which lithiasis is studied and treated. (Source: Clinical Proteomics)
Source: Clinical Proteomics - March 31, 2020 Category: Biochemistry Source Type: research

Early detection of Ebola virus proteins in peripheral blood mononuclear cells from infected mice
ConclusionsWhile mass spectrometry is not currently amenable to field diagnostics, these results suggest that viral protein enrichment in PBMCs in tandem with highly sensitive immunoassays platforms, could lead to the development of a rapid, high-throughput diagnostic platform for pre-symptomatic detection of EBOV infection. (Source: Clinical Proteomics)
Source: Clinical Proteomics - March 17, 2020 Category: Biochemistry Source Type: research

Urinary proteomics of Henoch-Sch önlein purpura nephritis in children using liquid chromatography-tandem mass spectrometry
ConclusionsOur study provides new insights into the assessment of HSPN progression in children, as well as new potential biomarkers. The data confirm the value of the urinary proteome in capturing the emergence of HSPN. (Source: Clinical Proteomics)
Source: Clinical Proteomics - March 12, 2020 Category: Biochemistry Source Type: research

The impact of ultraviolet- and infrared-based laser microdissection technology on phosphoprotein detection in the laser microdissection-reverse phase protein array workflow
AbstractReversible protein phosphorylation represents a key mechanism by which signals are transduced in eukaryotic cells. Dysregulated phosphorylation is also a hallmark of carcinogenesis and represents key drug targets in the precision medicine space. Thus, methods that preserve phosphoprotein integrity in the context of clinical tissue analyses are crucially important in cancer research. Here we investigated the impact of UV laser microdissection (UV LMD) and IR laser capture microdissection (IR LCM) on phosphoprotein abundance of key cancer signaling protein targets assessed by reverse-phase protein microarray (RPPA). ...
Source: Clinical Proteomics - March 9, 2020 Category: Biochemistry Source Type: research

The different expression of glycogen phosphorylases in renal clear cell renal carcinoma and chromophobe renal carcinoma
ConclusionWe found different expression of glycogen phosphorylases in CCRCC and CHRCC by quantitative proteomics, which provides potential therapeutic targets in the future. (Source: Clinical Proteomics)
Source: Clinical Proteomics - February 26, 2020 Category: Biochemistry Source Type: research

Correction to: Proteomic analysis of degradation ubiquitin signaling by ubiquitin occupancy changes responding to 26S proteasome inhibition
In the original publication of the article, Figure  2d was published incorrectly. The corrected Fig. 2 was given in this Correction article [1]. The original article has been corrected. (Source: Clinical Proteomics)
Source: Clinical Proteomics - February 21, 2020 Category: Biochemistry Source Type: research

Discovery of a putative blood-based protein signature associated with response to ALK tyrosine kinase inhibition
AbstractBackgroundALK tyrosine kinase inhibition has become a mainstay in the clinical management of ALK fusion positive NSCLC patients. Although ALK mutations can reliably predict the likelihood of response to ALK tyrosine kinase inhibitors (TKIs) such as crizotinib, they cannot reliably predict response duration or intrinsic/extrinsic therapeutic resistance. To further refine the application of personalized medicine in this indication, this study aimed to identify prognostic proteomic biomarkers in ALK fusion positive NSCLC patients to crizotinib.MethodsTwenty-four patients with advanced NSCLC harboring ALK fusion were a...
Source: Clinical Proteomics - February 7, 2020 Category: Biochemistry Source Type: research

Prediction of neoadjuvant chemotherapeutic efficacy in patients with locally advanced gastric cancer by serum IgG glycomics profiling
ConclusionWe here firstly present the profiling of IgGN-glycans in pretreatment serum of LAGC. The alterations in IgGN-glycome may be personalized biomarkers to predict the response to NACT in LAGC and help to illustrate the relationship between immunity and effect of NACT. (Source: Clinical Proteomics)
Source: Clinical Proteomics - February 6, 2020 Category: Biochemistry Source Type: research

Quantitative site- and structure-specific N-glycoproteomics characterization of differential N-glycosylation in MCF-7/ADR cancer stem cells
In this study, we report our comparative and quantitative site- and structure-specific N-glycoproteomics study of MCF-7/ADR cancer stem cells (CSCs) vs. MCF-7/ADR cells. With zic-HILIC enrichment, isotopic diethyl labeling, RPLC –MS/MS (HCD) analysis and GPSeeker DB search, differentially expressed N-glycosylation was quantitatively characterized at the intact N-glycopeptide level.Results4016 intact N-glycopeptides were identified with spectrum-level FDR  ≤ 1%. With the criteria of ≥ 1.5 fold change and p value 
Source: Clinical Proteomics - February 5, 2020 Category: Biochemistry Source Type: research

Proteomic analysis of degradation ubiquitin signaling by ubiquitin occupancy changes responding to 26S proteasome inhibition
ConclusionsIn summary, the computational method, previously described for glycosylation analysis, was used in this study for the assessment of ubiquitin stoichiometries and applied directly to proteomic data to distinguish degradation from non-degradation ubiquitin functions. (Source: Clinical Proteomics)
Source: Clinical Proteomics - January 25, 2020 Category: Biochemistry Source Type: research

The omics revolution: beyond genomics. A meeting report
AbstractThe “omics revolution: beyond genomics” satellite meeting, run under the auspices of the Australian Peptide Association, The Human Proteome Organisation (HUPO) and the HUPO Australia/New Zealand Chromosome 7 initiative, was held at the Oaks Resort, Port Douglas, Queensland, Australia, on 8th Septemb er 2019, immediately prior to the 13th Australian Peptide Conference. The meeting, which had over 100 participants representing Australasia, Europe and America, focused on recent advances in omics-related technologies, including mass spectrometry, biosensors and CryoEM, which will assist in the clin ical tra...
Source: Clinical Proteomics - January 24, 2020 Category: Biochemistry Source Type: research

Proteomics analysis of colon cancer progression
ConclusionNevertheless, the study has provided significant insights into CC stage progression for further investigation. (Source: Clinical Proteomics)
Source: Clinical Proteomics - December 28, 2019 Category: Biochemistry Source Type: research

The plasma peptides of breast versus ovarian cancer
AbstractBackgroundThere is a need to demonstrate a proof of principle that proteomics has the capacity to analyze plasma from breast cancer versus other diseases and controls in a multisite clinical trial design. The peptides or proteins that show a high observation frequency, and/or precursor intensity, specific to breast cancer plasma might be discovered by comparison to other diseases and matched controls. The endogenous tryptic peptides of breast cancer plasma were compared to ovarian cancer, female normal, sepsis, heart attack, Alzheimer ’s and multiple sclerosis along with the institution-matched normal and con...
Source: Clinical Proteomics - December 23, 2019 Category: Biochemistry Source Type: research

Quantitative proteome analysis of Merkel cell carcinoma cell lines using SILAC
ConclusionsThe results of this study present a new protein map of MCC and provide deeper insights in the biology of MCC. Data are available via ProteomeXchange with identifier PXD008181. (Source: Clinical Proteomics)
Source: Clinical Proteomics - December 19, 2019 Category: Biochemistry Source Type: research

Clinical method evaluation of hemoglobin S and C identification by top-down selected reaction monitoring and electron transfer dissociation
ConclusionsThis top-down SRM ETD method can be used in a clinical environment to detect Hb S and Hb C. (Source: Clinical Proteomics)
Source: Clinical Proteomics - December 17, 2019 Category: Biochemistry Source Type: research

The associations of self-rated health with cardiovascular risk proteins: a proteomics approach
ConclusionsPoor SRH was associated with raised concentrations of many plasma proteins. However, the relationships were largely attenuated by adjustments for CVD risk factors, comorbidity and psycho-social factors. Leptin and CCL20 were associated with poor SRH in the present study and could potentially be involved in the SRH –CVD link. (Source: Clinical Proteomics)
Source: Clinical Proteomics - November 18, 2019 Category: Biochemistry Source Type: research

Quantitative analysis of Mycobacterium avium subsp . hominissuis proteome in response to antibiotics and during exposure to different environmental conditions
AbstractMycobacterium avium subsp.hominissuis (MAH) belongs to the clinically important non-tuberculous mycobacterial group that infects immunocompromised patients and individuals with underling lung conditions. The need for prolonged therapy is a major challenge of MAH treatment, influencing the development of persistent and drug-resistant infections. The reason why bactericidal drugs take several months to eliminate MAH is unknown. To investigate MAH proteome remodeling under aerobic, anaerobic and biofilm conditions (as it is encountered in patient lungs) and identify metabolic changes potentially associated with bacter...
Source: Clinical Proteomics - November 13, 2019 Category: Biochemistry Source Type: research

iTRAQ-based quantitative proteomic analysis provides insight for molecular mechanism of neuroticism
ConclusionsOur study revealed the characteristics of the neurotic personality proteome, which might be intrinsic mechanism of the neurotic population. (Source: Clinical Proteomics)
Source: Clinical Proteomics - November 8, 2019 Category: Biochemistry Source Type: research

Matrisome analysis of intrahepatic cholangiocarcinoma unveils a peculiar cancer-associated extracellular matrix structure
ConclusionsOverall, this study contributes to the understanding of molecular basis underlying desmoplasia in iCCA and indicates the type III collagen as a promising therapeutic target. (Source: Clinical Proteomics)
Source: Clinical Proteomics - October 30, 2019 Category: Biochemistry Source Type: research

iTRAQ and PRM-based quantitative proteomics in early recurrent spontaneous abortion: biomarkers discovery
ConclusionsCD45, PSG1, and Prdx-2, were significantly dysregulated in the samples of ERSA and could become important biomarkers for the prediction and diagnosis of ERSA. Larger ‑scale studies are required to confirm the diagnostic value of these biomarkers. (Source: Clinical Proteomics)
Source: Clinical Proteomics - October 18, 2019 Category: Biochemistry Source Type: research

N -GlycositeAtlas: a database resource for mass spectrometry-based human N-linked glycoprotein and glycosylation site mapping
ConclusionsThe entire humanN-glycoproteome database as well as 22 sub-databases associated with individual tissues or body fluids can be downloaded from theN-GlycositeAtlas website athttp://nglycositeatlas.biomarkercenter.org. (Source: Clinical Proteomics)
Source: Clinical Proteomics - September 7, 2019 Category: Biochemistry Source Type: research

Potential early clinical stage colorectal cancer diagnosis using a proteomics blood test panel
ConclusionMS-based proteomics in combination with ultradepletion strategies have an immense potential of identifying diagnostic protein biosignature. (Source: Clinical Proteomics)
Source: Clinical Proteomics - August 28, 2019 Category: Biochemistry Source Type: research

iTRAQ plasma proteomics analysis for candidate biomarkers of type 2 incipient diabetic nephropathy
ConclusionsThese findings offer a theoretical basis for the early treatment of diabetic nephropathy. (Source: Clinical Proteomics)
Source: Clinical Proteomics - July 31, 2019 Category: Biochemistry Source Type: research

Screening differentially expressed proteins from co-cultured hematopoietic cells and bone marrow-derived stromal cells by quantitative proteomics (SILAC) method
ConclusionAltogether, we recommend such quantitative proteomics approach for the studies of the hematopoietic –stroma cross-talk, differentially expressed proteins and related signaling pathways identification. The differentially expressed proteins identified from this current SILAC method will provide a useful basis for ongoing studies of crosstalk between stromal cells and hematopoietic cells in co-cult ure systems. All these result suggested our ongoing studies can focus on the mechanisms underlying CKAP4 increase and CD44 decrease in co-cultured hematopoietic cells, and the increase of LCP1 and decrease of CAPG i...
Source: Clinical Proteomics - July 18, 2019 Category: Biochemistry Source Type: research

Predictive proteomic signatures for response of pancreatic cancer patients receiving chemotherapy
ConclusionBased on the cohort investigated, our data suggested that systemic proteome alterations involved in pathways associated with inflammation, immunoresponse, coagulation and complement cascades may be reporters of chemo-treatment outcome in PDAC patients. For the majority of the patients involved, the panel consisting of PZ, SHBG, VWF and CA 19-9 was able to segregate Good-responders from Limited-responders effectively. Our data also showed that dramatic fluctuations of biomarker concentration in the circulating system of a PDAC patient, which might result from biological heterogeneity or confounding complications, ...
Source: Clinical Proteomics - July 17, 2019 Category: Biochemistry Source Type: research

Correction to: A proteome-wide immuno-mass spectrometric identification of serum autoantibodies
In the original version of the article [1], an error was noticed under the heading “Immunoprecipitation on protein G magnetic beads” in “Methods” section. (Source: Clinical Proteomics)
Source: Clinical Proteomics - July 17, 2019 Category: Biochemistry Source Type: research

Lipid metabolism impairment in patients with sepsis secondary to hospital acquired pneumonia, a proteomic analysis
ConclusionProteomic analysis pointed to impairment of lipid metabolism as a major change in septic patients secondary to HAP, which was further validated by the reduced levels of cholesterol moieties and apolipoproteins in plasma. Our results stress the involvement of lipids in the pathogenesis of sepsis, which is in accordance with previous reports supporting the role of lipid moieties in pathogen toxin clearance and in modulating inflammatory responses. (Source: Clinical Proteomics)
Source: Clinical Proteomics - July 16, 2019 Category: Biochemistry Source Type: research

Discovering endometriosis biomarkers with multiplex cytokine arrays
ConclusionsThese findings show the utility and reliability of multiplex arrays in deciphering new biomarker panels for disease detection and may offer clues for understanding this mysterious disease. (Source: Clinical Proteomics)
Source: Clinical Proteomics - July 11, 2019 Category: Biochemistry Source Type: research

Correction to: Comprehensive proteome and phosphoproteome profiling shows negligible influence of RNAlater on protein abundance and phosphorylation
In the version of this article that was originally published [1], some information in the “Acknowledgements” section was omitted. (Source: Clinical Proteomics)
Source: Clinical Proteomics - July 11, 2019 Category: Biochemistry Source Type: research

Phenotyping multiple subsets in Sj ögren’s syndrome: a salivary proteomic SWATH-MS approach towards precision medicine
ConclusionsConstellations of proteins, including S100A proteins, characterize different pSS subsets reflecting either salivary gland dysfunction or inflammation. Salivary proteomics may foster future research projects ultimately aimed at developing personalized treatments for pSS patients. (Source: Clinical Proteomics)
Source: Clinical Proteomics - June 20, 2019 Category: Biochemistry Source Type: research

A proteome-wide immuno-mass spectrometric identification of serum autoantibodies
ConclusionsThis study demonstrates the effectiveness of a proteomic approach to identify serum autoantibody targets, using immunoaffinity purification followed by tandem mass spectrometry. Our methodology is applicable for proteome-wide analysis of autoantibody targets in a wide variety of clinical settings. (Source: Clinical Proteomics)
Source: Clinical Proteomics - June 20, 2019 Category: Biochemistry Source Type: research

Differential motility parameters and identification of proteomic profiles of human sperm cryopreserved with cryostraw and cryovial
ConclusionThe proteomic profiles of human sperm are greatly affected by cryopreservation with either type of CPC. GO analysis revealed that most of the differentially identified sperm proteins enriched in the extracellular membrane-bounded organelles, cytoplasm and cytosol. In addition, 106 susceptible proteins having known identities related to sperm functions were identified. In general, cryovial seems to be the preferred CPC for human sperm cryopreservation based on the post-thaw motility parameters and the effect on sperm proteomic profiles. These results are beneficial for the insight into the understanding of the cry...
Source: Clinical Proteomics - June 19, 2019 Category: Biochemistry Source Type: research

Elucidating the endogenous synovial fluid proteome and peptidome of inflammatory arthritis using label-free mass spectrometry
ConclusionsThe discovery-phase data generated herein has provided a basis for the identification of candidates with the greatest potential to serve as novel serum biomarkers specific to inflammatory arthritides. Moreover, these findings facilitate the understanding of possible disease mechanisms specific to each subtype. (Source: Clinical Proteomics)
Source: Clinical Proteomics - May 30, 2019 Category: Biochemistry Source Type: research

Plasma proteomic and autoantibody profiles reveal the proteomic characteristics involved in longevity families in Bama, China
ConclusionsProteomic and autoantibody profiles varied between the offspring of longevous and normal families which are from the same area and shared the same environmental factors. The identified differences were reported to be involved in several physiological and pathological pathways. The identified proteins will contribute to a better understanding of the proteomic characteristics of people from Bama longevous area and a revelation of the molecular mechanisms of longevity. (Source: Clinical Proteomics)
Source: Clinical Proteomics - May 20, 2019 Category: Biochemistry Source Type: research

Biomarkers of blood cadmium and incidence of cardiovascular events in non-smokers: results from a population-based proteomics study
ConclusionsB-Cd in non-smokers was associated with eight potential plasma biomarkers of CVD and kidney injury. The results suggest pathways for the associations between B-Cd and CVD and kidney injury. (Source: Clinical Proteomics)
Source: Clinical Proteomics - May 15, 2019 Category: Biochemistry Source Type: research

Stage-associated differences in the serum N - and O -glycan profiles of patients with non-small cell lung cancer
ConclusionsThe serum glycan profiles were significantly different between NSCLC and healthy control, and most of the glycosylation changes had occurred at early stage. Further evaluation is needed to examine the diagnostic value of the glycan markers identified in this study. (Source: Clinical Proteomics)
Source: Clinical Proteomics - May 10, 2019 Category: Biochemistry Source Type: research