Quantitation of β-tubulin isotype expression in taxane resistant human tumor tissue has been difficult to achieve because of the limited availability of validated antibodies. Here we present a label-free mass spectrometry method to quantitate relative expression levels of β–tubulin isotypes.
Using isotype specific reporter peptides, we determined relative β–tubulin isotype expression levels in human lung tumor tissue.
Four reporter peptides were chosen to quantitate the βI/βII, βIV, βIII and βV tubulin isotypes. These peptides were validated using human cancer cell lines. The label-free method was then used to determine β-tubulin isotype expression in nine human lung tumor samples, which had been described as high or low βIII-tubulin expressing using immunohistochemistry. It was found that βI/βII (accounting for 18.7%–65.7% of total β-tubulin) and βIVa/βIVb (26.3%–79.1%) were the most abundant isotypes and that the βIII (0–8.9%) and βV (1.0–10.4%) were less abundant in the tissue. We also categorized the samples as high or low βIII-tubulin expressing.
Conclusions and clinical relevance
With this method we can determine the relative expression levels of β-tubulin isotypes in human tumor tissue. This method will facilitate studies assessing the use of tubulin isotypes as biomarkers of taxane resistance.
β-tubulin isotypes; human lung tumors; label-free quantitation; mass spectrometry. taxane resistance
Proteomic analysis of formalin-fixed paraffin-embedded (FFPE) tissue offers significant diagnostic utility but is complicated due to the high level of covalently cross-linked proteins arising from formalin fixation. To address these challenges, we developed a reliable protein extraction method for FFPE tissue, based on heat-induced antigen retrieval within a pressure cooker. The protein extraction yield from archival FFPE tissue section is approximately 90% of that recovered from frozen tissue. This method demonstrates preservation of immuno-reactivity and recovery of full-length proteins by western blotting. Additionally we developed a well-based reverse-phase protein array platform utilizing an electrochemiluminescence detection system. Protein samples derived from FFPE tissue by means of laser capture dissection, with as few as 500 shots demonstrate measurable signal differences for different proteins. The lysates coated to the array plate, remain stable over 1 month at room temperature. Theses data suggest that this new protein-profiling platform coupled with the protein extraction method can be used for molecular profiling analysis in FFPE tissue, and contribute to the validation and development of biomarkers in clinical studies.
Formalin fixed; paraffin embedded tissue; Laser capture microdissection; Protein extraction; Reverse-phase protein array; Tissue lysate
The purpose of this study was to investigate naturally occurring C-peptide microheterogeneity in healthy and type 2 diabetes (T2D) populations.
MS immunoassays capable of simultaneously detecting intact C-peptide and variant forms were applied to plasma samples from 48 healthy individuals and 48 individuals diagnosed with T2D.
Common throughout the entire sample set were three previously unreported variations of C-peptide. The relative contribution of one variant, subsequently identified as C-peptide (3–31), was found to be more abundant in the T2D population as compared to the healthy population. Dipeptidyl peptidase IV is suspected to be responsible for this particular cleavage product, which is consistent with the pathophysiology of T2D.
Conclusions and clinical relevance
C-peptide does not exist in the human body as a single molecular species. It is qualitatively more heterogeneous than previously thought. These results lay a foundation for future studies devoted to a comprehensive understanding of C-peptide and its variants in healthy and diabetic populations.
C-peptide; Microheterogeneity; Population proteomics; Variants
Polymorphonuclear neutrophils (PMNs) play an important role in mediating the innate immune response after severe traumatic injury; however, the cellular proteome response to traumatic condition is still largely unknown.
We applied 2D-LC-MS/MS based shotgun proteomics to perform comparative proteome profiling of human PMNs from severe trauma patients and healthy controls.
A total of 197 out of ~2500 proteins (being identified with at least two peptides) were observed with significant abundance changes following the injury. The proteomics data were further compared with transcriptomics data for the same genes obtained from an independent patient cohort. The comparison showed that the protein abundance changes for the majority of proteins were consistent with the mRNA abundance changes in terms of directions of changes. Moreover, increased protein secretion was suggested as one of the mechanisms contributing to the observed discrepancy between protein and mRNA abundance changes. Functional analyses of the altered proteins showed that many of these proteins were involved in immune response, protein biosynthesis, protein transport, NRF2-mediated oxidative stress response, the ubiquitin-proteasome system, and apoptosis pathways.
CONCLUSIONS AND CLINICAL RELEVANCE
Our data suggest increased neutrophil activation and inhibited neutrophil apoptosis in response to trauma. The study not only reveals an overall picture of functional neutrophil response to trauma at the proteome level, but also provides a rich proteomics data resource of trauma-associated changes in the neutrophil that will be valuable for further studies of the functions of individual proteins in PMNs.
human neutrophil; LC-MS/MS; Proteomics; Trauma; Genomics
Although Crohn’s colitis (CC) and ulcerative colitis (UC) share several clinical features, they have different causes, mechanisms of tissue damage, and treatment options. Therefore, the accurate diagnosis is of paramount importance in terms of medical care. The distinction between UC/CC is made on the basis of clinical, radiologic, endoscopic, and pathologic interpretations but cannot be differentiated in up to 15% of IBD patients. Correct management of this “indeterminate colitis” (IC) depends on the accuracy of future, and yet not known, destination diagnosis (CC/UC).
We have developed a proteomic methodology that has the potential to discriminate between UC/CC. The histologic layers of 62 confirmed UC/CC tissues were analyzed using MALDI-MS for proteomic profiling.
A Support Vector Machine algorithm consisting of 25 peaks was able to differentiate spectra from CC and UC with 76.9% spectral accuracy when using a leave-20%-out cross validation. Application of the model to the entire data set resulted in accurate classification of 19/26 CC patients and 36/36 UC patients when using a 2/3 correct cutoff. A total 114 peaks were found to have Wilcoxin p-values of less than 0.05.
This information may provide new avenues for the development of novel personalized therapeutic targets.
Crohn’s colitis; Ulcerative colitis; Colon tissue profiling; Proteomics; Mass Spectrometry
Early diagnosis of primary immunodeficiency disorders (PIDD) is critical for maximizing patient survival and clinical outcomes. Consequently, there is significant interest in developing broad-based, high-throughput, screening approaches capable of utilizing small blood volumes to identify patients with PIDD.
We developed a novel proteomic screening approach using tandem mass spectrometry to simultaneously identify specific signature peptides derived from the transmembrane protein CD3ε and the intracellular proteins WASP and BTK as markers of three life-threatening PIDDs; Severe Combined Immunodeficiency (SCID), Wiskott-Aldrich syndrome (WAS) and X-Linked Agammaglobulinemia (XLA). Signature peptides were analyzed by LC/MS-MS in proteolytically digested lysates from cell lines and white blood cells. The amount of each peptide was determined by the ratio of the signature peptide peak area to that of a known amount of labeled standard peptide. Peptide concentrations were normalized to Actin.
We show that signature peptides from CD3ε, WASP, and BTK were readily detected in proteolytically digested cell lysate and their absence could correctly identify PIDD patients.
Conclusions and clinical relevance
This proof of concept study demonstrates the applicability of this approach to screen for PIDD and raises the possibility that it could be further multiplexed to identify additional PIDDs and potentially other disorders.
Primary Immunodeficiency; Severe Combined Immunodeficiency; X-linked Agammaglobulinemia; Wiskott-Aldrich Syndrome; Peptide Analysis; Tandem Mass Spectrometry
Protein signals obtained directly from frozen lung tissue sections using MALDI-MS were used to predict nodal involvement and survival in resected non-small cell lung cancer (NSCLC). We have identified a list of these protein signals and further evaluated their prognostic values for NSCLC using immunohistochemistry (IHC). Kaplan-Meier analysis was used to assess the mortality risk associated with the prognostic protein IHC-staining intensities. The combined IHC scores of calmodulin, thymosin β4, and thymosin β10 were found to be correlated with NSCLC patient survival (p = 0.004). Furthermore, low cofilin-1 IHC-staining intensity was found to be correlated with a better outcome for patients with negative lymph node status (p = 0.006) while high cofilin-1 IHC-staining intensity was found to be correlated with a better outcome for patients with positive node status (p = 0.034). In conclusion, the prognostic protein signals selected using MALDI-MS can be identified and tested by IHC in formalin-fixed tissue samples. MALDI-MS-derived protein signals can be potentially translated to a conventional clinical setting to aid in the prognosis of patients with NSCLC at the molecular level.
Biomarkers; Immunohistochemistry; MALDI-MS; Non-small cell lung cancer; Prognosis
The purpose of the work presented herein was to develop a high-throughput assay for the quantification of human insulin in plasma samples while simultaneously detecting, with high mass accuracy, any additional variant forms of insulin that might be present in each sample.
A mass spectrometric immunoassay (MSIA) was designed in which anti-human insulin antibodies were immobilized to commercially available MSIA pipette tips and used to capture insulin and related protein variants from human plasma.
Standard curves for insulin exhibited linearity (average R2 for three days of analysis = 0.99) and assay concentration limits of detection and limits of quantification for insulin were found to be 1 pM and 15 pM, respectively. Estimated CVs for interday experiments (n = 3 days) were < 8%. Simultaneously, the assay was shown to detect and identify insulin metabolites and synthetic insulin analogs (e.g. Lantus). Notably, insulin variants not known to exist in plasma were detected in diabetics.
CONCLUSIONS AND CLINICAL RELEVANCE
This introductory study sets a foundation towards the screening of large populations to investigate insulin isoforms, isoform frequencies, and their quantification.
insulin; microheterogeneity; population proteomics
Carbohydrates have fundamental roles throughout biology, yet they have not been as well studied as proteins and nucleic acids, in part due to limitations in the experimental tools. Improved methods for studying glycans could spur significant advances in the understanding and application of glycobiology. The use of affinity reagents such as lectins and glycan-binding antibodies is a valuable complement to methods involving mass spectrometry and chromatography. This article addresses two limitations that have prevented the broader experimental use of glycan-binding proteins: sensitivity and availability. The sensitivity limitation stems from the poor affinity that many glycan-binding proteins have as isolated analytical reagents. To address this problem, we propose making use of multivalent interactions between lectins and glycans, mimicking those frequently found in the biological setting. We have shown that a practical technique for producing lectin multimers can significantly improve detection sensitivity. The second limitation, availability, is the difficulty of finding and obtaining glycan-binding proteins that recognize less-common or arbitrarily defined glycan structures. To address this problem, we propose translating the wealth of existing glycan array data into a quantitative, searchable database of the specificities of glycan-binding proteins. Such a resource would allow us to more easily identify proteins with defined specificities and perform detailed comparisons between reagents. Solutions to these two limitations could lead to the more effective use of, and a broader range of, glycan-binding reagents.
Despite intensive treatment regimens, overall survival for high risk neuroblastoma (HRNB) is still poor. This is in part due to an inability to cure the disease once a patient has reached clinical relapse. Identifying plasma biomarkers of active disease may provide a way of relapse monitoring in HRNB.
In this study, we developed an integrated proteomic approach to identify plasma biomarkers for HRNB.
We identified seven candidate biomarkers (SAA, APOA1, IL-6, EGF, MDC, sCD40L and Eotaxin) for HRNB. These biomarkers were then used to create a multivariate classifier of HRNB, which showed a specificity of 90% (95%CI, 73%, 98%), and a sensitivity of 81% (95%CI, 54%, 96%) for classifying HRNB in a training set. When evaluated on independent test samples, the classifier exhibited 86% accuracy (95% CI, 42%, 100%) of identifying diagnostic samples, and 86% accuracy (95% CI, 70%, 100%) of detecting post-diagnosis longitudinal samples that having active disease.
Conclusion and clinical relevance
Further validation of these biomarkers may improve patients‘ outcomes by developing a simple blood test for the detection of relapse prior to the development of clinically evident disease. Understanding the role of these biomarkers in immune surveillance of neuroblastoma may also provide a new direction of therapeutic strategies.
Neuroblastoma; Relapse; Biomarkers; Cytokines; Chemokines
Improved monitoring of transplanted solid organs is one of the next crucial steps leading to an increase both patient and allograft survival. This can be facilitated through one or a set of surrogate biomarker molecules that accurately and precisely indicate the health status of the transplanted organ. Recent developments in the field of high throughput “omic” methods including genomics and proteomics have facilitated robust and comprehensive analysis of genes and proteins. This development has stimulated efforts in the identification of effective and clinically applicable gene and protein biomarkers in solid organ transplantation, including kidney transplantation. Some achievements have been made through proteomics in terms of profiling proteins and identification of potential biomarkers. However, the road to a successful biomarker discovery and its clinical implementation has proved to be challenging requiring a number of key issues to be addressed. Such issues are; the lack of widely accepted protocols, difficulty in sample processing and transportation and a lack of collaborative efforts to achieve significant sample sizes in clinical studies. In this review using our area of expertise, we describe the current strategies used for proteomic based biomarker discovery in renal transplantation, discuss inherent issues associated with these efforts and propose better strategies for successful biomarker discovery.
Urine; Proteomics; Peptidomics; Biomarker; organ transplantation; Acute rejection; Non-invasive biomarkers; Biomarker discovery
The present study is a discovery mode proteomics analysis of the membrane enriched fraction of post-mortem brain tissue from Alzheimer’s disease (AD) and control cases. This study aims to validate a method to identify new proteins that could be involved in the pathogenesis of AD and potentially serve as disease biomarkers.
Liquid chromatography-tandem mass spectrometry (LC-MS/MS) was used to analyze the membrane enriched fraction of human post-mortem brain tissue from five AD and five control cases of similar age. Biochemical validation of specific targets was performed by immunoblotting.
1709 proteins were identified from the membrane enriched fraction of frontal cortex. Label free quantification by spectral counting and G-test analysis identified 13 proteins that were significantly changed in disease. In addition to Tau (MAPT), two additional proteins found to be enriched in AD, Ubiquitin carboxy-terminal hydrolase 1 (UCHL1), and syntaxin binding protein 1 (Munc-18), were validated through immunoblotting.
Discussion and clinical relevance
Proteomic analysis of the membrane enriched fraction of post-mortem brain tissue identifies proteins biochemically altered in AD. Further analysis of this sub-proteome may help elucidate mechanisms behind AD pathogenesis and provide new sources of biomarkers.
Alzheimer’s disease; membrane enrichment; proteomics; neurodegeneration
The prognosis for children with IPAH unresponsive to therapy is poor. We investigated the plasma proteome for a molecular basis of good versus poor outcome to long-term vasodilator therapy.
Plasma was collected at baseline or shortly after therapy initiation and following chronic vasodilator therapy, then divided into those with good outcome (n = 8), and those with a poor outcome (n = 7). To identify proteins unique to either outcome, we used differential gel electrophoresis and mass spectrometry. Results were confirmed by commercial enzyme-linked immunosorbent assay.
Before and after therapy, SAA-4 was 4-fold lower in those with good outcome compared to those with poor outcome, while serum paraoxonase/arylesterase-1 was increased 2-fold in those with good outcome versus poor outcome. After therapy, haptoglobin and hemopexin were 1.45- and 1.8-fold lower, respectively, in those with a good versus poor outcome. Among those with a good outcome, SAP was 1.3-fold lower prior to therapy.
Conclusions and clinical relevance
SAP and SAA-4 regulate circulating mononuclear phagocytes. As such, they may contribute to the differential response to chronic vasodilator therapy in the context of inflammation in IPAH.
Inflammation; Pulmonary hypertension; Vasodilators
Salmonella bacteria cause millions of infections and thousands of deaths every year. This pathogen has an unusually broad host range including humans, animals, and even plants. During infection, Salmonella expresses a variety of virulence factors and effectors that are delivered into the host cell triggering cellular responses through protein–protein interactions (PPIs) with host cell proteins which make the pathogen’s invasion and replication possible. To speed up proteomic efforts in elucidating Salmonella–host interactomes, we carried out a survey of the currently published Salmonella–host PPI. Such a list can serve as the gold standard for computational models aimed at predicting Salmonella–host interactomes through integration of large-scale biological data sources. Manual literature and database search of >2200 journal articles and >100 databases resulted in a gold standard list of currently 62 PPI, including primarily interactions of Salmonella proteins with human and mouse proteins. Only six of these interactions were directly retrievable from PPI databases and 16 were highlighted in databases featuring literature extracts. Thus, the literature survey resulted in the most complete interactome available to date for Salmonella. Pathway analysis using Ingenuity and Broad Gene Set Enrichment Analysis (GSEA) software revealed among general pathways such as MAPK signaling in particular those related to cell death as well as cell morphology, turnover, and interactions, in addition to response to not only Salmonella but also other pathogenic – viral and bacterial – infections. The list of interactions is available at http://www.shiprec.org/indicationslist.htm
Interactome; Pathway analysis; Protein–protein interaction; Salmonella; Subnetwork analysis
The Quantitative Assay Database (QuAD), http://proteome.moffitt.org/QUAD/, facilitates widespread implementation of quantitative mass spectrometry in cancer biology and clinical research through sharing of methods and reagents for monitoring protein expression and modification.
Liquid chromatography coupled to multiple reaction monitoring mass spectrometry (LC-MRM) assays are developed using SDS-PAGE fractionated lysates from cancer cell lines. Pathway maps created using GeneGO Metacore provide the biological relationships between proteins and illustrate concepts for multiplexed analysis; each protein can be selected to examine assay development at the protein and peptide level.
The coupling of SDS-PAGE and LC-MRM screening has been used to detect 876 peptides from 218 cancer-related proteins in model systems including colon, lung, melanoma, leukemias, and myeloma, which has led to the development of 95 quantitative assays including stable-isotope labeled peptide standards. Methods are published online and peptide standards are made available to the research community. Protein expression measurements for heat shock proteins, including a comparison with ELISA and monitoring response to the HSP90 inhibitor, 17-DMAG, are used to illustrate the components of the QuAD and its potential utility.
Conclusions and Clinical Relevance
This resource enables quantitative assessment of protein components of signaling pathways and biological processes and holds promise for systematic investigation of treatment responses in cancer.
Cancer Biology; LC-MRM; Pathways; Quantification; Signaling
The aim of this study was to use on- tissue reduction followed by MALDI-IMS to identify an m/z 5812.85 peak which is over-expressed in healthy human pancreatic tissue compared to Type one Diabetes (T1D) tissue.
A major constraint of MALDI-IMS is identification of compounds with m/z ≥ 4000. On-tissue reduction using tris (2-carboxyethyl) phosphine (TCEP) breaks the inter-domain disulphide bonds generating low molecular weight peptides amenable to direct MS/MS analysis. Pancreatic tissues from healthy (n=1) and diabetic subjects (n=1) were profiled by MALDI-IMS with/without reduction.
On-tissue reduction resulted in the loss of the over expressed 5812.85 m/z peak and the simultaneous appearance of a 3430.664 m/z peak in healthy tissue. The latter peak presumably derived from the 5812.85 m/z peak was identified as the insulin B chain by MS/MS. MALDI-IMS images show that both the 5812.85 insulin peak before reduction and the 3430.664 peak after reduction co-localized with the healthy pancreatic islets.
Conclusion and clinical relevance
On-tissue reduction followed by MALDI-IMS resulted in the identification of insulin and localization of pancreatic islets of langerhans. The approach will be useful in the future identification of novel therapeutic molecular targets to beta-cells lost during T1D.
MALDI-IMS; Insulin; Βeta-cell; Disulphide bridge; Reduction
The development of insulin resistance and type 2 diabetes is determined by various factors, including defects within the insulin signaling pathway. Mediators of insulin resistance operate through activation of various protein kinase C (PKC) isoforms, IκB kinase β (IKKβ) and/or c-Jun N-terminal kinase (JNK), and subsequent inhibition of the proximal insulin signaling pathway via the insulin receptor substrate 1 (IRS1) and Akt. These mechanisms are still largely unresolved because of the complexity of the molecular events. In this study, an expression and activation state profiling of multiple known key signaling biomolecules involved in insulin metabolic and mitogenic signaling pathways was evaluated using a phosphospecific antibody array platform. The results of the arrayed antibodies were verified by the multiplexed bead array assay and conventional western blot analysis, and confirmed the well-known inhibitory effects of phorbol esters on insulin signaling pathway activation. Of interest, the increase in PKC signaling responses with phorbol esters was associated with activation of the lipid phosphatase PTEN and a 27 kDa heat shock protein. Thus, this insulin signaling antibody array provides a powerful and effective way to investigate the mechanism of insulin resistance and likely assist the development of innovative therapeutic drugs for type 2 diabetes.
Antibody array; insulin resistance; insulin signaling pathway; multiplexed bead array; phorbol 12-myristate 13-acetate (PMA)
Humoral immune responses play a pivotal role in naturally acquired immunity to malaria. Understanding which humoral responses are impaired among individuals at higher risk for malaria may improve our understanding of malaria immune control and contribute to vaccine development.
We compared humoral responses with 483 Plasmodium falciparum antigens between adults in, Kisumu (high, year-long malaria transmission leading to partial immunity), and adults in Kisii (low, seasonal malaria transmission). Then within each site, we compared malaria-specific humoral responses between those at higher risk for malaria (CD4+ ≤ 500) and those at lower risk for malaria (CD4+>500). A protein microarray chip containing 483 P. falciparum antigens and 71 HIV antigens was used. Benjamini–Hochberg adjustments were made to control for multiple comparisons.
Fifty-seven antigens including CSP, MSP1, LSA1 and AMA1 were identified as significantly more reactive in Kisumu than in Kisii. Ten of these antigens had been identified as protective in an earlier study. CD4+ T-cell count did not significantly impact humoral responses.
Protein microarrays are a useful method to screen multiple humoral responses simultaneously. This study provides useful clues for potential vaccine candidates. Modest decreases in CD4 counts may not significantly impact malaria-specific humoral immunity.
HIV-1; Humoral Immunity; Malaria; Vaccine
We present a strategy to survey proteolytic processes in human cancer microenvironments. By combining in situ microdialysis during cancer surgery and mass spectrometry we were able to identify proteolytic enzymes, protease inhibitors and cleavage products in the interstitial fluid surrounding tumors and anatomically matched normal sites. Protease activity-based 18O-profiling revealed peptides processed by co-collected proteases ex vivo. This approach provides unique views of proteolytic networks in human cancers that could aid biomarker discovery efforts.
Keyhole limpet hemocyanin (KLH) is used as a vaccine adjuvant, as a carrier protein for small haptens, and as a treatment for bladder cancer. Immunization with KLH produces antibodies to tumor-associated carbohydrate antigens in animals, and these antibodies have been postulated as the basis of efficacy for bladder cancer treatment. The purpose of this study was to evaluate antibody responses to KLH in humans.
A carbohydrate microarray was used to profile antibody responses in 14 individuals immunized with KLH plus alum adjuvant.
8/14 individuals produced antibodies to at least one tumor-associated carbohydrate antigen. Increases to Lewis X, Lewis Y, GA1di, GM3, and sialyl Lewis A were observed in certain individuals, but, in general, antibody profiles were highly variable. Pre-immunization antibody levels to a subset of array antigens had a statistically significant correlation with the magnitude of the antibody response to KLH.
Conclusions and Clinical Relevance
Antibodies to tumor-associated carbohydrate antigens can be produced in humans, but antibody profiles differ considerably from person to person, which may contribute to variable clinical responses with KLH. Pre-treatment antibody levels to certain antigens may be useful for predicting which patients will respond favorably to KLH.
Antibody; antigen array; glycan array; keyhole limpet hemocyanin; tumor-associated carbohydrate antigen
Kidney transplantation is the treatment of choice for end stage renal disease, with long term allograft loss being the major obstacle, and for which potential treatments are based on a histological diagnosis. The problem is that markers for predicting graft rejection are limited in number and invasive and quite non-specific. We have hypothesized that protein biomarkers might be discovered in the urine of patients when acute or chronic rejection might be occurring.
We have established a workflow in which initial screening for candidate biomarkers is first performed using urine samples on large scale antibody microarrays. This approach generated several dozen candidates. The next step is to qualify some of the strongest signals using the high throughput Reverse Capture Protein Microarray platform.
Four top candidates including ANXA11, Integrin α3 and Integrin β3, and TNFα initially identified by the antibody microarray platform were all qualified using Reverse Capture Protein Microarrays. We also used Receiver Operating Condition (ROC) curves to independently quantify the specificity and sensitivity of these four analytes.
Conclusions and clinical relevance
The present data suggest that these novel four analytes in the urine, together or independently, may contribute to a robust and quantitative urine proteomic signature for diagnosing acute or chronic rejection of renal allografts.
graft rejection; urine; proteomics; protein arrays
We generated extensive transcriptional and proteomic profiles from a Her2-driven mouse model of breast cancer that closely recapitulates human breast cancer. This report makes these data publicly available in raw and processed forms, as a resource to the community. Importantly, we previously made biospecimens from this same mouse model freely available through a sample repository, so researchers can obtain samples to test biological hypotheses without the need of breeding animals and collecting biospecimens.
Twelve datasets are available, encompassing 841 LC-MS/MS experiments (plasma and tissues) and 255 microarray analyses of multiple tissues (thymus, spleen, liver, blood cells, and breast). Cases and controls were rigorously paired to avoid bias.
In total, 18,880 unique peptides were identified (PeptideProphet peptide error rate ≤1%), with 3884 and 1659 non-redundant protein groups identified in plasma and tissue datasets, respectively. Sixty-one of these protein groups overlapped between cancer plasma and cancer tissue.
Conclusions and clinical relevance
These data are of use for advancing our understanding of cancer biology, for software and quality control tool development, investigations of analytical variation in MS/MS data, and selection of proteotypic peptides for MRM-MS. The availability of these datasets will contribute positively to clinical proteomics.
Breast cancer; Her2; mouse; proteome; transcriptome