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Journal articles on the topic 'Serum peptidome'

Author: Grafiati

Published: 4 June 2021

Last updated: 12 February 2022

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1

Fan, Nai-Jun, Chun-Fang Gao, Xiu-Li Wang, Guang Zhao, Qing-Yin Liu, Yuan-Yao Zhang, and Bao-Guo Cheng. "Serum Peptidome Patterns of Colorectal Cancer Based on Magnetic Bead Separation and MALDI-TOF Mass Spectrometry Analysis." Journal of Biomedicine and Biotechnology 2012 (2012): 1–8. http://dx.doi.org/10.1155/2012/985020.

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Background. Colorectal cancer (CRC) is one of the most common cancers in the world, identification of biomarkers for early detection of CRC represents a relevant target. The present study aims to determine serum peptidome patterns for CRC diagnosis.Methods. The present work focused on serum proteomic analysis of 32 health volunteers and 38 CRC by ClinProt Kit combined with mass spectrometry. This approach allowed the construction of a peptide patterns able to differentiate the studied populations. An independent group of serum (including 33 health volunteers, 34 CRC, 16 colorectal adenoma, 36 esophageal carcinoma, and 31 gastric carcinoma samples) was used to verify the diagnostic and differential diagnostic capability of the peptidome patterns blindly. An immunoassay method was used to determine serum CEA of CRC and controls.Results. A quick classifier algorithm was used to construct the peptidome patterns for identification of CRC from controls. Two of the identified peaks at m/z 741 and 7772 were used to construct peptidome patterns, achieving an accuracy close to 100% (>CEA,P<0.05). Furthermore, the peptidome patterns could differentiate validation group with high accuracy.Conclusions. These results suggest that the ClinProt Kit combined with mass spectrometry yields significantly higher accuracy for the diagnosis and differential diagnosis of CRC.

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2

Villanueva, Josep, John Philip, Lin DeNoyer, and Paul Tempst. "Data analysis of assorted serum peptidome profiles." Nature Protocols 2, no. 3 (March 2007): 588–602. http://dx.doi.org/10.1038/nprot.2007.57.

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3

Yang, Juan, Shuan-Ying Yang, Xiao-Yan Hu, Shu-Fen Huo, Wen-Li Shang, Zong-Fang Li, Lei Ni, et al. "Serum Peptidome Profiling in Patients with Lung Cancer." Anatomical Record: Advances in Integrative Anatomy and Evolutionary Biology 293, no. 12 (November 16, 2010): 2027–33. http://dx.doi.org/10.1002/ar.21267.

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4

Yang, Juan, Yong-Chun Song, Cheng-Xue Dang, Tu-Sheng Song, Zhi-Gang Liu, You-Min Guo, Zong-Fang Li, and Chen Huang. "Serum peptidome profiling in patients with gastric cancer." Clinical and Experimental Medicine 12, no. 2 (July 8, 2011): 79–87. http://dx.doi.org/10.1007/s10238-011-0149-2.

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5

Bai, Ju, Aili He, Wanggang Zhang, Yun Yang, Jianli Wang, Pengyu Zhang, Yuandong Feng, et al. "Serum Peptidome Based Multiple Myeloma Renal Impairment Biomarker Screening." Blood 126, no. 23 (December 3, 2015): 2968. http://dx.doi.org/10.1182/blood.v126.23.2968.2968.

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Abstract Background: Renal impairment (RI) is relatively common in patients with newly diagnosed MM (NDMM), ~20-40%, and forms one of the defining features for diagnosis of symptomatic disease. RI has a negative prognostic impact in patients with MM, with an increased risk of early death and a reduction in median survival of up to 50% compared with MM patients without RI. Identification of the early RI in MM and prompt intervention can effectively reverse the RI and prolong the survival of patients. Considering serum creatinine (SCr), blood urea nitrogen (BUN) and creatinine clearance (CrCl) are difficult to reflect early RI, cystatin C (Cys-C), as a new biomarker, has certain value for the diagnosis of early glomerular impairment in MM. However, the early stage of RI in MM was mainly renal tubular injury. Low molecular urine protein (retinol-binding protein, β-microglobulin) are effective in early renal tubular injury, but they are affected by urea PH value. This study was to screen a panel of serum peptides associated with early RI in MM. Methods: 164 MM patients were selected from those who were newly diagnosed in the Second Affiliated Hospital of Xi'an Jiao Tong University during a given period of time (2009.1-2014.1). Their diagnoses were made according to the diagnostic criteria from the International Myeloma Working Group. The median age was 65 years old (range 36-83) and 60.4% were male. RI was defined as having a CrCl<40ml/min. Weak cation exchange magnetic bead combined with matrix assisted laser desorption/ionization time of flight mass spectrometry were used to compare and analyze serum peptidome of MM with or without RI. Correlation analysis of two variables was estimated by Spearman method. The patients were categorized into two groups according to the relative intensities of peptides (≥mean versus <mean). Overall Survival was estimated by the Kaplan-Meier method and compared using a log-rank test. The event was defined as the time from initial diagnosis to treatment-related death time. Statistical significance was defined as p<0.05. Results: Serum peptidome of MM including 104 without RI and 50 with RI were analysed. 18 statistically different expressed peptide peaks were obtained in the molecular weight range of 700-10000Da (P<0.05), among which, 7 peptides were upregulated and 11 peptides were downregulated. Quick classifier (QC) model had optimal distinction efficiency, in the training set with a sensitivity of 93.33% and a specificity of 90%. Blind test verified that this model correctly identified 18 cases out of total 20 MM with RI and 70 cases from 74 MM without RI. Peptides with molecular weight of 3908.85Da and 3216.06Da were significant upregulated in MM patients with RI. Relative intensities of the two peptides were decreased when CrCl(38/50MM) was improved to 40ml/min after therapy. Peptide with molecular weight of 2990.08Da was significant downregulated in MM patients with RI. Its relative intensity was elevated after therapy(CrCl>40ml/min,38/50MM). Spearman correlation analysis showed that relative intensities of peptides with molecular weight of 3908.85Da, 3216.06Da and 2990.08Da were correlated with SCr(r=0.81, p<0.001; r=0.84, p<0.001; p=-0.86, p<0.001), CrCl(r=-0.79, p<0.001; r=-0.81, p<0.001; r=0.83, p<0.001), BUN(r=0.74, p<0.001; r=0.77, p<0.001; r=-0.79, p<0.001), Cys-C(r=0.81, p<0.001; r=0.84, p<0.001; r=-0.86, p<0.001). The median follow-up duration among 164 patients was 27 months (range 4-52 months). Kaplan-Meier analyses of overall survival (OS) showed that patients with higher relative intensities of peptide with 3908.85Da and 3216.06Da (≥mean relative intensity) had a significantly inferior outcome. Lower relative intensities of peptides with molecular weight of 3908.85Da and 3216.06Da (<mean relative intensity) was associated with a favorable OS (46.2±9.2% versus 16.1±6.5%, p=0.012; 41.7±9.5% versus 18.5±6.0%, P=0.021). The OS rate was higher in patients with increased relative intensity of peptides with molecular weight of 2990.08Da (≥mean relative intensity) of than in those with decreased relative intensity (<mean relative intensity)(36.1±10.5% versus 16.2±4.7%, p=0.008). Conclusion: Peptides(3908.85Da, 3216.06Da and 2990.08Da) associated with MM RI obtained by serum peptidome technology can provide new clue for early assess and diagnose MM RI in clinical. Disclosures No relevant conflicts of interest to declare.

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6

Zlotta, Alexandre R. "Differential Exoprotease Activities Confer Tumor-Specific Serum Peptidome Patterns." European Urology 49, no. 4 (April 2006): 756–57. http://dx.doi.org/10.1016/j.eururo.2006.02.005.

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7

Villanueva, J. "Differential exoprotease activities confer tumor-specific serum peptidome patterns." Journal of Clinical Investigation 116, no. 1 (December 8, 2005): 271–84. http://dx.doi.org/10.1172/jci26022.

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8

Zhou, Chun-Xue, Shi-Chen Xie, Man-Yao Li, Cui-Qin Huang, Huai-Yu Zhou, Hua Cong, Xing-Quan Zhu, and Wei Cong. "Analysis of the serum peptidome associated with Toxoplasma gondii infection." Journal of Proteomics 222 (June 2020): 103805. http://dx.doi.org/10.1016/j.jprot.2020.103805.

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9

Matysiak, Jan, Agata Światły, Joanna Hajduk, Joanna Matysiak, and Zenon Kokot. "Influence of Honeybee Sting on Peptidome Profile in Human Serum." Toxins 7, no. 5 (May 22, 2015): 1808–20. http://dx.doi.org/10.3390/toxins7051808.

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10

Gao, Yao, Lin Lin, Zhenzhen Huang, Yongjing Chen, and Wei Hang. "Peptidome workflow of serum and urine samples for biomarker discovery." Analytical Methods 3, no. 4 (2011): 773. http://dx.doi.org/10.1039/c0ay00705f.

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11

Dai, Xiaonan, Xuejing Song, Can Rui, Li Meng, Xuan Xue, Hongjuan Ding, Rong Shen, et al. "Peptidome Analysis of Human Serum From Normal and Preeclamptic Pregnancies." Journal of Cellular Biochemistry 118, no. 12 (June 9, 2017): 4341–48. http://dx.doi.org/10.1002/jcb.26087.

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12

OKANO, TETSUYA, MASAHIRO SEIKE, HIDEHIKO KURIBAYASHI, CHIE SOENO, TAKEO ISHII, KOZUI KIDA, and AKIHIKO GEMMA. "Identification of haptoglobin peptide as a novel serum biomarker for lung squamous cell carcinoma by serum proteome and peptidome profiling." International Journal of Oncology 48, no. 3 (January 11, 2016): 945–52. http://dx.doi.org/10.3892/ijo.2016.3330.

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13

Wang, Xusu, Guangquan Liu, Na Sheng, Mi Zhang, Xinxing Pan, Siyu Liu, Ke Huang, et al. "Peptidome characterization of ovarian cancer serum and the identification of tumor suppressive peptide ZYX36-58." Annals of Translational Medicine 8, no. 15 (August 2020): 925. http://dx.doi.org/10.21037/atm-20-2018.

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14

Klupczynska, Agnieszka, Agata Swiatly, Joanna Hajduk, Jan Matysiak, Wojciech Dyszkiewicz, Krystian Pawlak, and Zenon Kokot. "Identification of Serum Peptidome Signatures of Non-Small Cell Lung Cancer." International Journal of Molecular Sciences 17, no. 4 (March 31, 2016): 410. http://dx.doi.org/10.3390/ijms17040410.

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15

Ma, Ying, Yanmei Hou, Binsong Han, Kui Xie, Lina Zhang, and Peng Zhou. "Peptidome comparison following gastrointestinal digesta of bovine versus caprine milk serum." Journal of Dairy Science 104, no. 1 (January 2021): 47–60. http://dx.doi.org/10.3168/jds.2020-18471.

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16

Liotta, L. A. "Serum peptidome for cancer detection: spinning biologic trash into diagnostic gold." Journal of Clinical Investigation 116, no. 1 (December 8, 2005): 26–30. http://dx.doi.org/10.1172/jci27467.

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17

Padoan, Andrea. "The Impact of Pre-Analytical Conditions on Human Serum Peptidome Profiling." PROTEOMICS - Clinical Applications 12, no. 3 (March 15, 2018): 1700183. http://dx.doi.org/10.1002/prca.201700183.

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18

Caoxuebin, Yangyanling. "ISCHEAMIC CARDIOMYOPATHY PATIENTS WITH HEART FAILURE—SPECIFIC SERUM PEPTIDOME PATTERN RESEARCH." Heart 98, Suppl 2 (October 2012): E168.2—E168. http://dx.doi.org/10.1136/heartjnl-2012-302920j.25.

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19

Fan, Nai-Jun, Chun-Fang Gao, Guang Zhao, Xiu-Li Wang, and Liang Qiao. "Serum peptidome patterns for early screening of esophageal squamous cell carcinoma." Biotechnology and Applied Biochemistry 59, no. 4 (July 2012): 276–82. http://dx.doi.org/10.1002/bab.1024.

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20

Rovithi, Maria, Joline S. Lind, Thang V. Pham, Jaco C. Knol, Henk M. W. Verheul, Egbert F. Smit, and Connie R. Jimenez. "Response prediction by MALDI-TOF-MS serum peptide profiling of combination treatment with sorafenib and erlotinib in patients with non-small cell lung cancer." Journal of Clinical Oncology 30, no. 15_suppl (May 20, 2012): e18094-e18094. http://dx.doi.org/10.1200/jco.2012.30.15_suppl.e18094.

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e18094 Background: Mass spectrometry can be used to generate diagnostic peptide peak profiles "signatures" of serum samples1. Peak profiles can be used to compare different sera and correlate samples (i.e., patient groups) with clinical data to assist in diagnosis, monitoring, and/or prediction. Indeed, in recent studies, we and other researchers have successfully combined serum peptide profiling by mass spectrometry (MS) with bioinformatics and have established distinctive serum polypeptide MS patterns that correlate with cancer types and clinically relevant outcomes2. We performed serum peptide profiling of patients with advanced stage non-small cell lung cancer (NSCLC) treated with erlotinib and sorafenib in a previously reported clinical trial at baseline, after one week of treatment, and after three weeks of treatment, to establish treatment efficacy signatures. Methods: Using automated magnetic C18 bead-assisted serum peptide capture coupled to matrix-assisted laser desorption/ ionization time of flight mass spectrometry (MALDI-TOF MS), serum peptide profiling1 of 50 NSCLC patients was conducted and peptide mass profiles (spectra) obtained. Data analyses of pretreatment serum peptide profiles, as well as dynamic changes in peptide abundance during treatment, were performed to establish support-vector machine-based algorithms that can predict treatment efficacy. Results: A 13 ion-peptide signature could discriminate with a sensitivity of 93% and specificity of 71% a training group of patients with short progression free survival (n=14) and long progression free survival (n=14). The signature shows discriminative power for the remaining non-overlapping set of 22 patients, as well as for the complete dataset of 50 patients. Pattern analysis of overall responses and toxicity is ongoing. Conclusions: Serum peptidome profiling using MALDI-TOF-MS coupled to pattern diagnostics may provide biomarkers predictive of response to targeted treatment in patients with NSCLC, thus enabling pretreatment selection of appropriate subgroups.

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21

Fiedler, Georg Martin, Alexander Benedikt Leichtle, Julia Kase, Sven Baumann, Uta Ceglarek, Klaus Felix, Tim Conrad, et al. "Serum Peptidome Profiling Revealed Platelet Factor 4 as a Potential Discriminating Peptide Associated with Pancreatic Cancer." Clinical Cancer Research 15, no. 11 (May 26, 2009): 3812–19. http://dx.doi.org/10.1158/1078-0432.ccr-08-2701.

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22

Ai, Tingting, Feng Chen, Shaonan Zhou, Jieni Zhang, Hui Zheng, Yanheng Zhou, Wei Hu, Xiaofei Liu, Li Li, and Jiuxiang Lin. "Magnetic Bead-Based Serum Peptidome Profiling in Patients with Gestational Diabetes Mellitus." BioMed Research International 2015 (2015): 1–8. http://dx.doi.org/10.1155/2015/586309.

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Gestational diabetes mellitus (GDM) is a frequent medical condition during pregnancy. Early diagnosis and treatment of GDM are crucial for both the mother and the baby. In the present study, we aimed to identify specific biomarkers to assist in the early detection of GDM and give some clues to the possible causes of GDM by comparing serum peptide profile differences between GDM patients and healthy controls. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) was used in combination with weak cation exchange magnetic bead (WCX-MB). Levels of four peptides (4418.9, 2219.7, 2211.5, and 1533.4 Da) were significantly different. Interestingly, three of them (4418.9, 2211.5, and 1533.4 Da) were identified when GDM patients with two degrees of glucose intolerance were compared. Additionally, peptides 2211.5 and 1533.4 Da showed a decreasing trend as glucose intolerance increased, while peptide 4418.9 Da exhibited the reverse tendency. In conclusion, our study provides novel insights into the altered serum peptide profile of GDM patients. The specific candidate biomarkers may contribute to the development of GDM.

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23

Zapico-Muñiz, Edgar, Antoni Farré-Viladrich, Nayra Rico-Santana, Francesc González-Sastre, and Josefina Mora-Brugués. "Standardized Peptidome Profiling of Human Serum for the Detection of Pancreatic Cancer." Pancreas 39, no. 8 (November 2010): 1293–98. http://dx.doi.org/10.1097/mpa.0b013e3181dfcbe5.

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Yan, Ling, Jia Yi, Changwu Huang, Jian Zhang, Shuhui Fu, Zhijie Li, Qian Lyu, et al. "Rapid Detection of COVID-19 Using MALDI-TOF-Based Serum Peptidome Profiling." Analytical Chemistry 93, no. 11 (March 3, 2021): 4782–87. http://dx.doi.org/10.1021/acs.analchem.0c04590.

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25

Ziganshin, Rustam, Georgii Arapidi, Igor Azarkin, Elena Zaryadieva, Dmitry Alexeev, Vadim Govorun, and Vadim Ivanov. "New method for peptide desorption from abundant blood proteins for plasma/serum peptidome analyses by mass spectrometry." Journal of Proteomics 74, no. 5 (May 2011): 595–606. http://dx.doi.org/10.1016/j.jprot.2011.01.014.

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26

Sirolli, Vittorio, Luisa Pieroni, Lorenzo Di Liberato, Andrea Urbani, and Mario Bonomini. "Urinary Peptidomic Biomarkers in Kidney Diseases." International Journal of Molecular Sciences 21, no. 1 (December 21, 2019): 96. http://dx.doi.org/10.3390/ijms21010096.

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In order to effectively develop personalized medicine for kidney diseases we urgently need to develop highly accurate biomarkers for use in the clinic, since current biomarkers of kidney damage (changes in serum creatinine and/or urine albumin excretion) apply to a later stage of disease, lack accuracy, and are not connected with molecular pathophysiology. Analysis of urine peptide content (urinary peptidomics) has emerged as one of the most attractive areas in disease biomarker discovery. Urinary peptidome analysis allows the detection of short and long-term physiological or pathological changes occurring within the kidney. Urinary peptidomics has been applied extensively for several years now in renal patients, and may greatly improve kidney disease management by supporting earlier and more accurate detection, prognostic assessment, and prediction of response to treatment. It also promises better understanding of kidney disease pathophysiology, and has been proposed as a “liquid biopsy” to discriminate various types of renal disorders. Furthermore, proteins being the major drug targets, peptidome analysis may allow one to evaluate the effects of therapies at the protein signaling pathway level. We here review the most recent findings on urinary peptidomics in the setting of the most common kidney diseases.

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27

Mostovenko, Ekaterina, Samantha Saunders, Pretal P. Muldoon, Lindsey Bishop, Matthew J. Campen, Aaron Erdely, and Andrew K. Ottens. "Carbon Nanotube Exposure Triggers a Cerebral Peptidomic Response: Barrier Compromise, Neuroinflammation, and a Hyperexcited State." Toxicological Sciences 182, no. 1 (April 21, 2021): 107–19. http://dx.doi.org/10.1093/toxsci/kfab042.

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Abstract The unique physicochemical properties of carbon nanomaterials and their ever-growing utilization generate a serious concern for occupational risk. Pulmonary exposure to these nanoparticles induces local and systemic inflammation, cardiovascular dysfunction, and even cognitive deficits. Although multiple routes of extrapulmonary toxicity have been proposed, the mechanism for and manner of neurologic effects remain minimally understood. Here, we examine the cerebral spinal fluid (CSF)-derived peptidomic fraction as a reflection of neuropathological alterations induced by pulmonary carbon nanomaterial exposure. Male C57BL/6 mice were exposed to 10 or 40 µg of multiwalled carbon nanotubes (MWCNT) by oropharyngeal aspiration. Serum and CSFs were collected 4 h post exposure. An enriched peptide fraction of both biofluids was analyzed using ion mobility-enabled data-independent mass spectrometry for label-free quantification. MWCNT exposure induced a prominent peptidomic response in the blood and CSF; however, correlation between fluids was limited. Instead, we determined that a MWCNT-induced peptidomic shift occurred specific to the CSF with 292 significant responses found that were not in serum. Identified MWCNT-responsive peptides depicted a mechanism involving aberrant fibrinolysis (fibrinopeptide A), blood-brain barrier permeation (homeobox protein A4), neuroinflammation (transmembrane protein 131L) with reactivity by astrocytes and microglia, and a pro-degradative (signal transducing adapter molecule, phosphoglycerate kinase), antiplastic (AF4/FMR2 family member 1, vacuolar protein sorting-associated protein 18) state with the excitation-inhibition balance shifted to a hyperexcited (microtubule-associated protein 1B) phenotype. Overall, the significant pathologic changes observed were consistent with early neurodegenerative disease and were diagnostically reflected in the CSF peptidome.

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Nicolardi, Simone, Berit Velstra, Bart J. Mertens, Bert Bonsing, Wilma E. Mesker, Rob A. E. M. Tollenaar, André M. Deelder, and Yuri E. M. van der Burgt. "Ultrahigh resolution profiles lead to more detailed serum peptidome signatures of pancreatic cancer." Translational Proteomics 2 (March 2014): 39–51. http://dx.doi.org/10.1016/j.trprot.2013.12.003.

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29

He, Kun, Xin-Yu Wen, Ai-Ling Li, Tao Li, Jie Wang, Hong-Xia Wang, and Na Wang. "Serum Peptidome Variations in a Healthy Population: Reference to Identify Cancer-Specific Peptides." PLoS ONE 8, no. 5 (May 8, 2013): e63724. http://dx.doi.org/10.1371/journal.pone.0063724.

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Yin, Lingfeng, Yingying Huai, Chun Zhao, Hongjuan Ding, Tao Jiang, and Zhonghua Shi. "Early Second-Trimester Peptidomic Identification of Serum Peptides for Potential Prediction of Gestational Diabetes Mellitus." Cellular Physiology and Biochemistry 51, no. 3 (2018): 1264–75. http://dx.doi.org/10.1159/000495538.

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Background/Aims: Early screening and diagnosis is important for minimizing gestational adverse outcomes. Routine screening of gestational diabetes mellitus (GDM) at 24–28 weeks with 75 g oral glucose challenge test (OGCT) leaves limited time for intervention and prevention. This study aims to analyze maternal serum peptides in the early second-trimester for prediction of gestational diabetes mellitus (GDM). Methods: Serum samples were collected from 16-18-week pregnant women that visited Nanjing Maternity and Child Health Care Hospital from April to August 2015. According to gestational outcome with or without GDM in late pregnancy, 200 of serum samples from GDM mothers and controls were randomly divided into two subgroups. Peptidomic identification of serum peptides was performed by combining ultrafiltration and liquid chromatography-tandem mass spectrometry (LC-MS/MS) to investigate the differentially-expressed peptides between two groups. Results: A total of 297 identified peptides, originating from 228 proteins, were significantly differentially expressed in the GDM group compared with control. These precursor proteins may play critical roles in cell death of cortical neurons, elongation of cellular protrusions, and stabilization of microtubules. Major networks identified included those involving lipid metabolism, molecular transport and small molecule biochemistry. Conclusion: We provide for the first time a validated peptidome profile of early second-trimester serum in normal and GDM mothers, and we investigated the potential serum biomarkers for GDM. We concluded that 297 peptides could serve as potential biomarkers for GDM.

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Wan, Qing-Lian, Xiang-Sheng Hou, and Guang Zhao. "Utility of Serum Peptidome Patterns of Esophageal Squamous Cell Carcinoma Patients for Comprehensive Treatment." Asian Pacific Journal of Cancer Prevention 14, no. 5 (May 30, 2013): 2919–23. http://dx.doi.org/10.7314/apjcp.2013.14.5.2919.

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Hashiguchi, Teruto, Kenji Tanaka, Lyang-Ja Lee, Ken Sasaki, Shoji Natsugoe, Ko-ichi Kawahara, Kimiyoshi Arimura, and Ikuro Maruyama. "Diagnostic value of serum peptidome analyses for protease activated pathological conditions beyond cancer diagnosis." Medical Hypotheses 73, no. 5 (November 2009): 760–63. http://dx.doi.org/10.1016/j.mehy.2009.04.026.

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Yang, Juan, Yanni Chen, Xiaofan Xiong, Xiaobo Zhou, Lin Han, Lei Ni, Wenjing Wang, et al. "Peptidome Analysis Reveals Novel Serum Biomarkers for Children with Autism Spectrum Disorder in China." PROTEOMICS - Clinical Applications 12, no. 5 (May 30, 2018): 1700164. http://dx.doi.org/10.1002/prca.201700164.

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Timms, John F., Rainer Cramer, Stephane Camuzeaux, Ali Tiss, Celia Smith, Brian Burford, Ilia Nouretdinov, et al. "Peptides Generated Ex Vivo from Serum Proteins by Tumor-Specific Exopeptidases Are Not Useful Biomarkers in Ovarian Cancer." Clinical Chemistry 56, no. 2 (February 1, 2010): 262–71. http://dx.doi.org/10.1373/clinchem.2009.133363.

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Abstract Background: The serum peptidome may be a valuable source of diagnostic cancer biomarkers. Previous mass spectrometry (MS) studies have suggested that groups of related peptides discriminatory for different cancer types are generated ex vivo from abundant serum proteins by tumor-specific exopeptidases. We tested 2 complementary serum profiling strategies to see if similar peptides could be found that discriminate ovarian cancer from benign cases and healthy controls. Methods: We subjected identically collected and processed serum samples from healthy volunteers and patients to automated polypeptide extraction on octadecylsilane-coated magnetic beads and separately on ZipTips before MALDI-TOF MS profiling at 2 centers. The 2 platforms were compared and case control profiling data analyzed to find altered MS peak intensities. We tested models built from training datasets for both methods for their ability to classify a blinded test set. Results: Both profiling platforms had CVs of approximately 15% and could be applied for high-throughput analysis of clinical samples. The 2 methods generated overlapping peptide profiles, with some differences in peak intensity in different mass regions. In cross-validation, models from training data gave diagnostic accuracies up to 87% for discriminating malignant ovarian cancer from healthy controls and up to 81% for discriminating malignant from benign samples. Diagnostic accuracies up to 71% (malignant vs healthy) and up to 65% (malignant vs benign) were obtained when the models were validated on the blinded test set. Conclusions: For ovarian cancer, altered MALDI-TOF MS peptide profiles alone cannot be used for accurate diagnoses.

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Rico Santana, Naira, Edgar Zapico Muñiz, Dolores Cocho, Yolanda Bravo, Raquel Delgado Mederos, and Joan Martí-Fàbregas. "Analysis of Peptidome Profiling of Serum from Patients with Early Onset Symptoms of Ischemic Stroke." Journal of Stroke and Cerebrovascular Diseases 23, no. 2 (February 2014): 235–40. http://dx.doi.org/10.1016/j.jstrokecerebrovasdis.2013.01.002.

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Bai, Ju, Yun Yang, Jianli Wang, Wanggang Zhang, Lei Zhang, Fangxia Wang, Xiaman Wang, et al. "Serum Peptidome Based Biomarkers Searching for Monitoring Minimal Residual Disease in Adult Acute Monocytic Leukemia." Blood 128, no. 22 (December 2, 2016): 5233. http://dx.doi.org/10.1182/blood.v128.22.5233.5233.

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Abstract Background: Acute monocytic leukemia (M5) is one common type in acute myeloid leukemia (AML). The present study found that a few M5 had special reproducible chromosomal abnormalities and molecular abnormalities. The heterogeneity and complexity of M5 lead to lack of specific tumor-associated markers for molecular diagnosis and targeted therapy. CLINPROT system, with unique advantages, is a firenew and distinctive proteomics technology and has been widely used in the researches of solid tumor and hemopathic malignancies. This study was to screen a panel of serum peptides associated with M5 different disease states for molecular diagnosis and monitoring minimal residual disease. Methods: 92 M5 were enrolled for the study from those who were newly diagnosed (ND) in the Second Affiliated Hospital of Xi'an Jiao Tong University from January 2009 to July 2014. The median age was 45 years old (range 18-73) and 57.6% were male. Diagnosis was made according to bone marrow cell morphology, cytochemical staining and cellular immune phenotype. 90 healthy cases (HC) (age range 19-70, median age 43 years old, male/female 51/39) were recruited from those who came to our hospital to undergo healthy physical examination and had no any abnormal symptoms and results. Sera of 92 M5 were gained pre- and post-treatment of chemotherapy. Weak cation exchange magnetic bead combined with matrix assisted laser desorption/ ionization time of flight mass spectrometry were used to compare and analyze serum peptidome of M5 with different disease states. Spearman method was used to do correlation analysis of two variables. Statistical significance was defined as p<0.05. Results: A total of 42 peptides in the molecular weight range of 700-10000 Da were detected using ClinProt system and statistically different between adult M5 and healthy controls. Among them, 9 peptides were elevated and 33 were decreased in M5. Genetic algorithm (GA) was used to obtain a diagnostic model consisting of 6 peptides that could discriminate M5 from controls with a high sensitivity (100%) and specificity (96.67%). Mass charge ratios (m/z) were 6041.91, 4662.15, 7823.02, 9210.97, 1108.91 and 3263.37 respectively. Blind test verified that this model correctly identified 60 cases out of total 62 M5 and 57 cases from 60 healthy controls. The relative intensities of peptides with m/z of 6041.91 and 4662.15 were increased in the ND group and non-complete remission (CR) group, when comparing with the CR group and HC group(p=0.002; p<0.001), but there was no significant difference between the two groups for any of the peptides (p=0.27, p=0.31). No significant difference was found between the CR group and HC group (p=0.22, p=0.41). The relative intensities of peptides with m/z of 7823.02, 9210.97, 1108.91 and 3263.37 were reduced in the ND group and non-CR group when comparing with the CR group and HC group (p<0.001, p=0.0023, p=0.004, p<0.001), and the two groups had no significant difference (p=0.26, p=0.09, p=0.32, p=0.61). No significant difference was observed between the HC group and CR group (p=0.52, p=0.35, p=0.17, p=0.73). Spearman correlation analysis showed that relative intensities of peptides with m/z of 4662.15, 7823.02 and 9210.97 were correlated with high white blood cells (r=0.88, p<0.001; r=-0.89, p<0.001; p=-0.87, p<0.001), FLT3 mutation (r=0.90, p<0.001; r=-0.87, p<0.001; r=-0.88, p<0.001) , extramedullary disease (r=0.80, p<0.001; r=-0.86, p<0.001; r=- 0.82, p<0.001). The relative intensities of the other three peptides had weak correlation with the unfavorable clinical features of M5 at diagnosis. Conclusion: This panel of peptides has encouraging efficiency in discriminating M5 from HCs and potential value in monitoring M5 minimal residual disease. Disclosures No relevant conflicts of interest to declare.

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Gianazza, Erica, Clizia Chinello, Veronica Mainini, Marta Cazzaniga, Valeria Squeo, Giancarlo Albo, Stefano Signorini, et al. "Alterations of the serum peptidome in renal cell carcinoma discriminating benign and malignant kidney tumors." Journal of Proteomics 76 (December 2012): 125–40. http://dx.doi.org/10.1016/j.jprot.2012.07.032.

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Ke, Li, He Wei-Hua, Fan Nai-Jun, Gao Chun-Fang, Zhao Guang, Sun Gao-Bin, and Zheng Guo-Bao. "Serum peptidome patterns of hepatocellular carcinoma based on magnetic bead separation and mass spectrometry analysis." Turkish Journal of Gastroenterology 25, no. 1 (April 22, 2015): 147–52. http://dx.doi.org/10.5152/tjg.2014.4888.

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Fan, Nai-Jun, Chun-Fang Gao, Guang Zhao, Xiu-Li Wang, and Qing-Yin Liu. "Serum peptidome patterns of breast cancer based on magnetic bead separation and mass spectrometry analysis." Diagnostic Pathology 7, no. 1 (2012): 45. http://dx.doi.org/10.1186/1746-1596-7-45.

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Liu, Yun, Fangqiao Wei, Feng Wang, Changdong Li, Ge Meng, Hua Duan, Qingwei Ma, and Weiyuan Zhang. "Serum peptidome profiling analysis for the identification of potential biomarkers in cervical intraepithelial neoplasia patients." Biochemical and Biophysical Research Communications 465, no. 3 (September 2015): 476–80. http://dx.doi.org/10.1016/j.bbrc.2015.08.042.

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Forones, Nora Manoukian, Talita Mendes de Oliveira, Jose Thales Lacerda, Meiriellen Dias, Maria Anita Mendes, and Maria Aparecida Juliano. "Integrating endogenous peptides analysis and protease mapping for identification of potential serum biomarkers in gastric adenocarcinoma." Journal of Clinical Oncology 37, no. 15_suppl (May 20, 2019): e15564-e15564. http://dx.doi.org/10.1200/jco.2019.37.15_suppl.e15564.

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e15564 Background: Gastric cancer (GC) is the third cause of cancer death in the world. In Brazil 21.000 new cases had been diagnosed in 2018 and the mortality rate is associated with late diagnosis that contributed to poor prognosis. The objective was to study endogenous peptides in serum of patients with GC. Methods: Fifteen serum samples of patients with diagnosis of gastric adenocarcinoma (TNM stage I-IV) and 15 controls were included. Endogenous peptides were extracted and pooled of random mode in 5 biological replicates (n = 3 samples) for each group. The mixture peptides was submitted to nLC-MS/MS analysis and peptide sequences identified were used to protease mapping. Results: A total of 191 peptides (≥ 7 amino acids) were identified corresponding to 36 proteins involved mainly on metabolic and immune system processes, signal transduction, platelet and neutrophils degranulation. Peptidome-based protease mapping identified 59 proteases (29 serine-, 19 metallo-, 8 cisteine- and 3 aspartic-), in which Prothrombin, Plasminogen, MMP14, MMP7 and MMP3 proteases yielded most of peptides. Twenty sequences derived from Fibrinogen A, Fibrinogen B, Complement C3 (C3f), Apolipoprotein A-I (N-terminal), Prothrombin (C-terminal of Activation peptide fragment 2; N-terminal of Thrombin light chain) and Coagulation factor XIII A (N-terminal) were significantly different (p ≤ 0.5). Between these peptides, 14 were up regulated and six downregulated in GC patients. The phosphopeptide 20ADSpGEGDFLAEGGGVR35 (Fibrinopeptide A) was significantly increased (p< 0.03) in GC serum samples, while the non-phosphorylated Fibrinopeptide A was decreased (p<0.04), suggesting a higher phosphorylation rate in this protein in GC patients. Further, the peptide 31QGVNDNEEGFFSAR44 (Fibrinopeptide B) was downregulated (p<0.04) in GC serum samples; in counterpart, the Fibrinopeptide B derived peptides NDNEEGFF (p<0.0007) and QGVNDNEEGFFS (p<0.0013) was up regulated, suggesting a higher proteolysis in GC serum samples. Conclusions: The investigation of protease/substrate activity relationship may be described such as a novel panorama for discovery of serum biomarkers.

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Hortin, Glen L. "The MALDI-TOF Mass Spectrometric View of the Plasma Proteome and Peptidome." Clinical Chemistry 52, no. 7 (July 1, 2006): 1223–37. http://dx.doi.org/10.1373/clinchem.2006.069252.

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Abstract Background: Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and the related technique, surface-enhanced laser desorption/ionization (SELDI)-TOF MS, are being applied widely to analyze serum or plasma specimens for potential disease markers. Methods: Reports on the basic principles and applications of MALDI-TOF MS were reviewed and related to information on abundance and masses of major plasma proteins. Outcomes: MALDI-TOF MS is a particle-counting method that responds to molar abundance, and ranking of plasma proteins by molar abundance increases the rank of small proteins relative to traditional ranking by mass abundance. Detectors for MALDI-TOF MS augment the bias for detecting smaller components by yielding stronger signals for an equivalent number of small vs large ions. Consequently, MALDI-TOF MS is a powerful tool for surveying small proteins and peptides comprising the peptidome or fragmentome, opening this new realm for analysis. It is complementary to techniques such as electrophoresis and HPLC, which have a bias for detecting larger molecules. Virtually all of the potential markers identified by MALDI-TOF MS to date represent forms of the most abundant plasma proteins. Conclusions: Analyses of serum or plasma by MALDI-TOF MS provide new information mainly about small proteins and peptides with high molar abundance. The spectrum of observed proteins and peptides suggests value for applications such as assessment of cardiovascular risk, nutritional status, liver injury, kidney failure, and systemic immune responses rather than early detection of cancer. Extending analysis by MALDI-TOF MS to lower abundance components, such as markers for early-stage cancers, probably will require more extensive specimen fractionation before analysis.

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Zhang, Juan, Kehong Tan, Xing Meng, Wenwen Yang, Haiyan Wei, Rongli Sun, Lihong Yin, and Yuepu Pu. "Overexpression of G6PD and HSP90 Beta in Mice with Benzene Exposure Revealed by Serum Peptidome Analysis." International Journal of Environmental Research and Public Health 12, no. 9 (September 10, 2015): 11241–53. http://dx.doi.org/10.3390/ijerph120911241.

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Abe, Koji, Jingwei Shang, Xiaowen Shi, Toru Yamashita, Nozomi Hishikawa, Mami Takemoto, Ryuta Morihara, et al. "A New Serum Biomarker Set to Detect Mild Cognitive Impairment and Alzheimer’s Disease by Peptidome Technology." Journal of Alzheimer's Disease 73, no. 1 (January 7, 2020): 217–27. http://dx.doi.org/10.3233/jad-191016.

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Yang, Juan, Yong-Chun Song, Tu-Sheng Song, Xiao-Yan Hu, You-Min Guo, Zong-Fang Li, Cheng-Xue Dang, and Chen Huang. "Identification of Novel Low Molecular Weight Serum Peptidome Biomarkers for Non-Small Cell Lung Cancer (NSCLC)." Journal of Clinical Laboratory Analysis 26, no. 3 (May 2012): 148–54. http://dx.doi.org/10.1002/jcla.21502.

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Bai, Ju, Aili He, Wanggang Zhang, Chen Huang, Juan Yang, Yun Yang, Jianli Wang, and Yang Zhang. "Potential biomarkers for adult acute myeloid leukemia minimal residual disease assessment searched by serum peptidome profiling." Proteome Science 11, no. 1 (2013): 39. http://dx.doi.org/10.1186/1477-5956-11-39.

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Wang, Hao, Chenghua Luo, Shengtao Zhu, Honghong Fang, Qing Gao, Siqi Ge, Haixia Qu, et al. "Serum peptidome profiling for the diagnosis of colorectal cancer: discovery and validation in two independent cohorts." Oncotarget 8, no. 35 (July 26, 2017): 59376–86. http://dx.doi.org/10.18632/oncotarget.19587.

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Gil, Geun-Cheol, Jim Brennan, Dan J. Throckmorton, Steven S. Branda, and Gabriela S. Chirica. "Automated analysis of mouse serum peptidome using restricted access media and nanoliquid chromatography–tandem mass spectrometry." Journal of Chromatography B 879, no. 15-16 (May 2011): 1112–20. http://dx.doi.org/10.1016/j.jchromb.2011.03.028.

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Wakabayashi, Ichiro, Naomi Mambo, Takahiro Ueda, Daisuke Nonaka, Lyang-Ja Lee, Kenji Tanaka, and Joji Kotani. "New Biomarkers for Prediction of Disseminated Intravascular Coagulation in Patients With Sepsis." Clinical and Applied Thrombosis/Hemostasis 24, no. 9_suppl (October 10, 2018): 223S—229S. http://dx.doi.org/10.1177/1076029618804078.

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Complication of disseminated intravascular coagulation (DIC) is a determinant of the prognosis for patients with sepsis. The purpose of this study was to find DIC-related peptides in blood for prediction and early diagnosis of DIC in patients with sepsis. The participants were 20 patients with sepsis (age: 68.9 ± 11.4 years) and they were divided into 2 groups with (n = 8) and without (n = 12) a complication of DIC. Peptides in the serum of the patients were inclusively analyzed by a new method for peptidome analysis using a target plate, BLOTCHIP. By differential analysis of peptides in the blood from patients in the groups with and without DIC, we selected 13 mass spectrometry (MS) peaks as candidate marker peptides for prediction of DIC. By subsequent MS/MS structural analysis, 8 peptides were successfully identified as marker peptides for DIC in patients with sepsis. The peptides were fragments of serum amyloid A-2 protein, α2-HS-glycoprotein, fibrinogen α chain, fibrinogen β chain, serum albumin, collagen α1 (I) chain, collagen α1 (III) chain, and coagulation factor XIII A chain. In receiver–operating characteristic analysis for the relationships between the marker peptides and DIC, the area under the curve for each of these peptides was 0.594 to 0.760. We identified 8 blood marker peptides for prediction of DIC complication in patients with sepsis. Further studies by direct measurements of the serum peptide levels in larger numbers of patients with sepsis-induced DIC are needed to confirm the findings of this study.

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Beitia, Maider, Paolo Romano, Gorka Larrinaga, Jon Danel Solano-Iturri, Annalisa Salis, Gianluca Damonte, Marco Bruzzone, Marcello Ceppi, and Aldo Profumo. "The Activation of Prothrombin Seems to Play an Earlier Role than the Complement System in the Progression of Colorectal Cancer: A Mass Spectrometry Evaluation." Diagnostics 10, no. 12 (December 11, 2020): 1077. http://dx.doi.org/10.3390/diagnostics10121077.

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Colorectal cancer (CRC) is the second cause of death in men and the third in women. This work deals with the study of the low molecular weight protein fraction of sera from patients who underwent surgery for CRC and who were followed for several years thereafter. MALDI-TOF MS was used to identify serum peptidome profiles of healthy controls, non-metastatic CRC patients and metastatic CRC patients. A multiple regression model was applied to signals preliminarily selected by SAM analysis to take into account the age and gender differences between the groups. We found that, while a signal m/z 2021.08, corresponding to the C3f fragment of the complement system, appears significantly increased only in serum from metastatic CRC patients, a m/z 1561.72 signal, identified as a prothrombin fragment, has a significantly increased abundance in serum from non-metastatic patients as well. The findings were also validated by a bootstrap resampling procedure. The present results provide the basis for further studies on large cohorts of patients in order to confirm C3f and prothrombin as potential serum biomarkers. Thus, new and non-invasive tests might be developed to improve the classification of colorectal cancer.

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