UniSpec: Deep Learning for Predicting the Full Range of Peptide Fragment Ion Series to Enhance the Proteomics Data Analysis Workflow.

We present UniSpec, an attention-driven deep neural network designed to predict comprehensive collision-induced fragmentation spectra, thereby improving peptide identification in shotgun proteomics. Utilizing a training data set of 1.8 million unique high-quality tandem mass spectra (MS2) from 0.8 million unique peptide ions, UniSpec learned with a peptide fragmentation dictionary encompassing 7919 fragment peaks. Among these, 5712 are neutral loss peaks, with 2310 corresponding to modification-specific neutral losses. Remarkably, UniSpec can predict 73%-77% of fragment intensities based on our NIST reference library spectra, a significant leap from the 35%-45% coverage of only b and y ions. Comparative studies with Prosit elucidate that while both models are strong at predicting their respective fragment ion series, UniSpec particularly shines in generating more complex MS2 spectra with diverse ion annotations. The integration of UniSpec's predictions into shotgun proteomics data analysis boosts the identification rate of tryptic peptides by 48% at a 1% false discovery rate (FDR) and 60% at a more confident 0.1% FDR. Using UniSpec's predicted in-silico spectral library, the search results closely matched those from search engines and experimental spectral libraries used in peptide identification, highlighting its potential as a stand-alone identification tool. The source code and Python scripts are available on GitHub (https://github.com/usnistgov/UniSpec) and Zenodo (https://zenodo.org/records/10452792), and all data sets and analysis results generated in this work were deposited in Zenodo (https://zenodo.org/records/10052268).

Does the weekend effect exist for acute type A aortic dissection?-a retrospective case-control study.

Background: The weekend effect refers to the mortality difference for patients admitted/operated on weekends compared to those on weekdays. The study aimed to provide new evidence on the impact of the weekend effect on acute type A aortic dissection (ATAAD). Methods: Primary endpoints were operative mortality, stroke, paraplegia, and continuous renal replacement therapy (CRRT). A meta-analysis of current evidence on the weekend effect was first conducted. Analyses based on single-center data (retrospective, case-control study) were further performed. Results: A total of 18,462 individuals were included in the meta-analysis. The pooled results showed that mortality was not significantly higher for ATAAD on weekends compared to that on weekdays [odds ratio (OR): 1.16, 95% CI: 0.94-1.43]. The single-center cohort included 479 patients, which also showed no significant differences in primary and secondary outcomes between the two groups. The unadjusted OR for weekend group over weekday group was 0.90 (95% CI: 0.40-1.86, P=0.777). The adjusted OR for weekend group was 0.94 (95% CI: 0.41-2.02, P=0.880) controlling for significant preoperative factors, and 0.75 (95% CI: 0.30-1.74, P=0.24) controlling for significant preoperative and operative factors altogether. In PSM matched cohort, the operative mortality was still comparable between the weekend group [10 (7.2%)] and weekday group [9 (6.5%)] (P=1.000). No significant survival difference was observed between the two groups (P=0.970). Conclusions: The weekend effect was not found to be applicable to ATAAD. However, clinicians should be cautious of the weekend effect as it is disease-specific and may vary across healthcare systems.

Less Is More: Surgical Phase Recognition From Timestamp Supervision.

Surgical phase recognition is a fundamental task in computer-assisted surgery systems. Most existing works are under the supervision of expensive and time-consuming full annotations, which require the surgeons to repeat watching videos to find the precise start and end time for a surgical phase. In this paper, we introduce timestamp supervision for surgical phase recognition to train the models with timestamp annotations, where the surgeons are asked to identify only a single timestamp within the temporal boundary of a phase. This annotation can significantly reduce the manual annotation cost compared to the full annotations. To make full use of such timestamp supervisions, we propose a novel method called uncertainty-aware temporal diffusion (UATD) to generate trustworthy pseudo labels for training. Our proposed UATD is motivated by the property of surgical videos, i.e., the phases are long events consisting of consecutive frames. To be specific, UATD diffuses the single labelled timestamp to its corresponding high confident (i.e., low uncertainty) neighbour frames in an iterative way. Our study uncovers unique insights of surgical phase recognition with timestamp supervision: 1) timestamp annotation can reduce 74% annotation time compared with the full annotation, and surgeons tend to annotate those timestamps near the middle of phases; 2) extensive experiments demonstrate that our method can achieve competitive results compared with full supervision methods, while reducing manual annotation costs; 3) less is more in surgical phase recognition, i.e., less but discriminative pseudo labels outperform full but containing ambiguous frames; 4) the proposed UATD can be used as a plug-and-play method to clean ambiguous labels near boundaries between phases, and improve the performance of the current surgical phase recognition methods. Code and annotations obtained from surgeons are available at https://github.com/xmed-lab/TimeStamp-Surgical.

Surgical repair of unilateral absence of pulmonary artery in children with pulmonary hypertension: a single-center retrospective study.

Background: The early diagnosis of unilateral absence of pulmonary artery (UAPA) in children offers an opportunity for effective intervention. Due to the lack of clinical evidence, a consensus regarding surgical treatment has yet to be reported. The aim of this study is to evaluate the effectiveness and safety of pulmonary artery (PA) reconstruction with a "two-segment" technique to repair UAPA in patients with pulmonary hypertension. Methods: Intraoperatively, the ligamentum arteriosum connecting the innominate artery and distal PA was dissected and occluded. A conduit created by fresh autologous pericardium formed the first "segment" of the neo-PA. The second "segment" was a Gore vascular graft with integrated rings anastomosed between the proximal end of the pericardial conduit and the main pulmonary artery (MPA). Results: A total of five consecutive patients were included, and the absent PA was successfully reconstructed using the "two-segment" technique in all patients. Following revascularization, the direct measurement of the pressure in MPA during the operation showed that the average mean pulmonary artery pressure (mPAP) decreased from 31.3±16.0 to 16.8±4.2 mmHg (P=0.047). The average mPAP/radial mean arterial pressure (rMAP) ratio decreased from 0.59±0.27 preoperatively to 0.30±0.10 postoperatively (P=0.028). The mean follow-up period was 18.85±4.67 months. The median diameter of the reconstructed PA (pericardial segment) measured by transthoracic echocardiography (TTE) was 6.1 mm. One patient safely underwent a redo operation to repair relative stenosis in the neo-PA. Conclusions: Early PA reconstruction may effectively alleviate pulmonary hypertension in children with UAPA. The "two-segment" technique is safe and can facilitate potential redo pulmonary arterioplasty. Anticoagulation and antiplatelet therapy, as well as frequent follow-up, is required after the operation.

Structure-Based Molecular Networking for the Discovery of Anti-HBV Compounds from Saussurea lappa (Decne.) C.B Clarke.

It is a crucial to find target compounds in natural product research. This study presents a concept of structure-guided isolation to find candidate active molecules from herbs. We establish a process of anti-viral sesquiterpene networking. An analysis of the networking suggested that new anti-HBV sesquiterpene may be attributable to eudesmane-, guaiane-, cadinane-, germacane- and bisabolane-type sesquiterpenes. In order to evaluate the efficiency of the structure-based molecular networking, ethanol extract of Saussurea lappa (Decne.) C.B Clarke was investigated, which led to the isolation of two guaiane-type (1 and 14), ten eudesmane-type (2-5 and 8-13), two chain (6 and 7) and one germacrane-type (15) sesquiterpenes, including seven new ones, lappaterpenes A-G (1-7), which are reported on herein. The absolute configurations of the new compounds were established by coupling constants, calculated ECD and ROESY correlations, as well as comparisons of optical rotation values with those of known compounds. The absolute configuration of compound 2 was further confirmed by X-ray diffraction. Compounds 1-15 were evaluated for their potency against hepatitis B virus. Compounds 4, 6, 7 and 9 showed effect on HBsAg with inhibition ratios of more than 40% at 30 µM concentrations. Compounds 14 and 15 inhibited HBsAg secretion with the values of IC50 0.73 ± 0.18 and 1.43 ± 0.54 µM, respectively. Structure-based molecular networking inspired the discovery of target compounds.

Proguanil synergistically sensitizes ovarian cancer cells to olaparib by increasing DNA damage and inducing apoptosis.

Ovarian cancer is the second leading cause of cancer-related deaths in women, with low five-year survival rates. Therefore, it is essential to seek new treatment options. Olaparib, a PARP inhibitor, has benefited many ovarian cancer patients, but olaparib is much less effective as a single agent in 50% of patients with high grade severe tumors. Proguanil, which was originally developed as an anti-malarial drug, has gained attention due to its anti-tumor effects. Here, we evaluated the anti-tumor effect of the combination of olaparib and proguanil on ovarian cancer cells, aimed to develop a potential medical option for treating ovarian cancer patients. We examined the effect on proliferation by MTT and colony formation assays, while cell migration was measured by the transwell assay. The effect on apoptosis was measured by flow cytometry and AO/EB staining assays. Western blotting was used to detect protein expression levels in cells treated with olaparib and/or proguanil. In addition, the synergistic effect of these two drugs is calculated by CompuSyn software. The combination of olaparib and proguanil significantly increased growth suppression and apoptosis in ovarian cancer cells, compared to either single agent alone. Furthermore, results showed that the combination of olaparib and proguanil synergistically increased olaparib-induced apoptosis and DNA damage and reduced the efficiency of DNA homologous recombination repair. Our findings indicate that combination of olaparib with proguanil will be a novel potential administration route for treating ovarian cancer patients.

Phenformin synergistically sensitizes liver cancer cells to sorafenib by downregulating CRAF/ERK and PI3K/AKT/mTOR pathways.

Sorafenib is a first-line drug to treat advanced hepatocellular carcinoma (HCC), which can prolong the median overall survival of patients by approximately 3 months. Phenformin is a biguanide derivative that has been shown to exhibit antitumor activity superior to that of metformin. We herein explored the ability of phenformin to enhance the anti-cancer activity of sorafenib against HCC and the mechanisms underlying such synergy. The Hep-G2 and SMMC-7721 HCC cell lines were treated with sorafenib and/or phenformin, after which the proliferation of these cells was evaluated via MTT and colony formation assays, while invasion and apoptotic cell death were evaluated via Transwell and flow cytometry assays, respectively. In addition, protein levels were assessed by Western blotting, drug synergy was assessed with the CompuSyn software, and xenograft models were established by implanting Hep-G2 cells into nude mice and then assessing drug antitumor efficacy. Sorafenib and phenformin exhibited a synergistic ability to suppress HCC cell proliferation, migration, and survival. Phenformin further bolstered the ability of sorafenib to inhibit the CRAF/ERK and PI3K/AKT/mTOR pathways. Strikingly, the combination of these two drugs achieved better in vivo efficacy in a murine model system, without causing significant weight loss or hepatorenal toxicity. Sorafenib and phenformin can synergistically suppress CRAF/ERK and PI3K/AKT/mTOR pathway activation in HCC cells, and may thus represent a promising approach to treating this deadly cancer.

Phenformin and ataxia-telangiectasia mutated inhibitors synergistically co-suppress liver cancer cell growth by damaging mitochondria.

Inhibitors of ataxia-telangiectasia mutated (ATM), such as KU-55933 (Ku), represent a promising class of novel anticancer drugs. In addition, the biguanide derivative phenformin exhibits antitumor activity superior to that of the AMPK activator metformin. Herein, we assessed the potential combinatorial therapeutic efficacy of phenformin and Ku when used to inhibit the growth of liver cancer cells, and we assessed the mechanisms underlying such efficacy. The Hep-G2 and SMMC-7721 liver cancer cell lines were treated with phenformin and Ku either alone or in combination, after which the impact of these drugs on cellular proliferation was assessed via 3-(4,5-dimethylthiazol) 2, 5-diphenyltetrazolium and colony formation assays, whereas Transwell assays were used to gauge cell migratory activity. The potential synergy between these two drugs was assessed using the CompuSyn software, while flow cytometry was employed to evaluate cellular apoptosis. In addition, western blotting was utilized to measure p-ATM, p-AMPK, p-mTOR, and p-p70s6k expression, while mitochondrial functionality was monitored via morphological analyses, JC-1 staining, and measurements of ATP levels. Phenformin and Ku synergistically impacted the proliferation, migration, and apoptotic death of liver cancer cells. Together, these compounds were able to enhance AMPK phosphorylation while inhibiting the phosphorylation of mTOR and p70s6k. These data also revealed that phenformin and Ku induced mitochondrial dysfunction as evidenced by impaired ATP synthesis, mitochondrial membrane potential, and abnormal mitochondrial morphology. These findings suggest that combination treatment with phenformin and Ku may be an effective approach to treating liver cancer via damaging mitochondria within these tumor cells.

Comprehensive Analysis of Tryptic Peptides Arising from Disulfide Linkages in NISTmAb and Their Use for Developing a Mass Spectral Library.

This work presents methods for identifying and then creating a mass spectral library for disulfide-linked peptides originating from the NISTmAb, a reference material of the humanized IgG1k monoclonal antibody (RM 8671). Analyses involved both partially reduced and non-reduced samples under neutral and weakly basic conditions followed by nanoflow liquid chromatography tandem mass spectrometry (LC-MS/MS). Spectra of peptides containing disulfide bonds are identified by both MS1 ion and MS2 fragment ion data in order to completely map all the disulfide linkages in the NISTmAb. This led to the detection of 383 distinct disulfide-linked peptide ions, arising from fully tryptic cleavage, missed cleavage, irregular cleavage, complex Met/Trp oxidation mixtures, and metal adducts. Fragmentation features of disulfide bonds under low-energy collision dissociation were examined. These include (1) peptide bond cleavage leaving disulfide bonds intact; (2) disulfide bond cleavage, often leading to extensive fragmentation; and (3) double cleavage products resulting from breakages of two peptide bonds or both peptide and disulfide bonds. Automated annotation of various complex MS/MS fragments enabled the identification of disulfide-linked peptides with high confidence. Peptides containing each of the nine native disulfide bonds were identified along with 86 additional disulfide linkages arising from disulfide bond shuffling. The presence of shuffled disulfides was nearly completely abrogated by refining digest conditions. A curated spectral library of 702 disulfide-linked peptide spectra was created from this analysis and is publicly available for free download. Since all IgG1 antibodies have the same constant regions, the resulting library can be used as a tool for facile identification of "hard-to-find" disulfide-bonded peptides. Moreover, we show that one may identify such peptides originating from IgG1 proteins in human serum, thereby serving as a means of monitoring the completeness of protein reduction in proteomics studies. Data are available via ProteomeXchange with identifier PXD023358.

Mass Spectral Library of Acylcarnitines Derived from Human Urine.

We describe the creation of a mass spectral library of acylcarnitines and conjugated acylcarnitines from the LC-MS/MS analysis of six NIST urine reference materials. To recognize acylcarnitines, we conducted in-depth analyses of fragmentation patterns of acylcarnitines and developed a set of rules, derived from spectra in the NIST17 Tandem MS Library and those identified in urine, using the newly developed hybrid search method. Acylcarnitine tandem spectra were annotated with fragments from carnitine and acyl moieties as well as neutral loss peaks from precursors. Consensus spectra were derived from spectra having similar retention time, fragmentation pattern, and the same precursor m/z and collision energy. The library contains 157 different precursor masses, 586 unique acylcarnitines, and 4 332 acylcarnitine consensus spectra. Furthermore, from spectra that partially satisfied the fragmentation rules of acylcarnitines, we identified 125 conjugated acylcarnitines represented by 987 consensus spectra, which appear to originate from Phase II biotransformation reactions. To our knowledge, this is the first report of conjugated acylcarnitines. The mass spectra provided by this work may be useful for clinical screening of acylcarnitines as well as for studying relationships among fragmentation patterns, collision energies, structures, and retention times of acylcarnitines. Further, these methods are extensible to other classes of metabolites.

Methylation of the ataxia telangiectasia mutated gene (ATM) promoter as a radiotherapy outcome biomarker in patients with hepatocellular carcinoma.

The goal of this study was to evaluate the contribution of ataxia telangiectasia mutated (ATM) gene promoter methylation to hepatocellular carcinoma (HCC) and the predictive value of radiotherapy outcome. ATM promoter methylation status was detected using methylation-specific PCR in 118 HCC, 50 adjacent liver, and 20 normal liver samples. PCR products were verified by bisulfite sequencing PCR. ATM expression was detected by quantitative PCR (qPCR) and immunohistochemistry (IHC) in 50 paired HCC and adjacent normal tissues and 68 locally advanced HCC biopsy tissues. Furthermore, radiotherapy outcomes in 68 locally advanced HCC patients were determined using European Association for the Study of Liver criteria and survival analysis. The results revealed that the methylation frequency of the ATM promoter was significantly higher in HCC tissues than in normal liver tissues (χ = 16.830, P < .001). Quantitative PCR (qPCR) and IHC results showed a significant association between ATM promoter methylation and ATM expression in HCC (χ = 10.510, P < .001), and methylated ATM was correlated with lower ATM expression compared with unmethylated ATM (r = 0.356, P < .001). Furthermore, methylation of the ATM promoter was significantly associated with superior outcomes in patients with locally advanced HCC who initially received radiotherapy. Together, these results indicate that ATM promoter methylation might increase the risk of HCC by regulating ATM expression, and thus may function as a potential biomarker for predicting radiotherapy outcomes in HCC patients.

Hybrid Search: A Method for Identifying Metabolites Absent from Tandem Mass Spectrometry Libraries.

Metabolomics has a critical need for better tools for mass spectral identification. Common metabolites may be identified by searching libraries of tandem mass spectra, which offers important advantages over other approaches to identification. But tandem libraries are not nearly complete enough to represent the full molecular diversity present in complex biological samples. We present a novel hybrid search method that can help identify metabolites not in the library by similarity to compounds that are. We call it "hybrid" searching because it combines conventional, direct peak matching with the logical equivalent of neutral-loss matching. A successful hybrid search requires the library to contain "cognates" of the unknown: similar compounds with a structural difference confined to a single region of the molecule, that does not substantially alter its fragmentation behavior. We demonstrate that the hybrid search is highly likely to find similar compounds under such circumstances.

Mass Spectrometry Fingerprints of Small-Molecule Metabolites in Biofluids: Building a Spectral Library of Recurrent Spectra for Urine Analysis.

A large fraction of ions observed in electrospray liquid chromatography-mass spectrometry (LC-ESI-MS) experiments of biological samples remain unidentified. One of the main reasons for this is that spectral libraries of pure compounds fail to account for the complexity of the metabolite profiling of complex materials. Recently, the NIST Mass Spectrometry Data Center has been developing a novel type of searchable mass spectral library that includes all recurrent unidentified spectra found in the sample profile. These libraries, in conjunction with the NIST tandem mass spectral library, allow analysts to explore most of the chemical space accessible to LC-MS analysis. In this work, we demonstrate how these libraries can provide a reliable fingerprint of the material by applying them to a variety of urine samples, including an extremely altered urine from cancer patients undergoing total body irradiation. The same workflow is applicable to any other biological fluid. The selected class of acylcarnitines is examined in detail, and derived libraries and related software are freely available. They are intended to serve as online resources for continuing community review and improvement.

[Effect of down-regulation of fatty acid synthase expression on proliferation, migration and invasion of bladder carcinoma UMUC3 cell lines].

OBJECTIVE: To investigate the effects of fatty acid synthase (FASN) on proliferation, migration and invasion of bladder cancer UMUC3 cell lines and possible mechanism. METHODS: The expression levels of FASN protein in 30 cases of bladder cancer and 15 cases of normal bladder tissues were detected by Immunohistochemistry. FASN siRNA and nonsense siRNA were transfected into UMUC3 cell lines by lipofectamine 2000 respectively, and the stable siFASN and siControl cell lines were successfully obtained after screening and identification for several times. The siFASN cell lines were set as the experimental group, while the siControl cell lines were set as the control group. The expressions of FASN protein and mRNA in the experimental group and the control group were detected by Western blot and real-time quantitative PCR (RT-PCR) respectively. Cell proliferation activities in two groups were detected by MTT assay and cell invasion and migration in two groups were detected by cell scratch test and Transwell invasive assays respectively. RESULTS: FASN protein was overexpressed in bladder cancer tissues, and it was closely correlated with pathological stage and grade (P＜0.05). Compared with the siControl group, the expressions of FASN mRNA and protein in the siFASN group cell lines were decreased significantly (P＜0.05). The cell proliferation ability, the migration ability and the number of transmembrane cells of siFASN group cell lines were reduced significantly (P＜0.05). CONCLUSION: The FASN overexpression may play an essential role in the development and progression of bladder cancer. Down-regulation of FASN expression can inhibit the proliferation, migration and invasion of bladder cancer cells, and inhibition of FASN expression is expected to be a new treatment for bladder cancer.

Left minimally invasive esophagectomy in a patient with synchronous esophageal and lung cancers: Case report.

RATIONALE: Minimally invasive esophagectomy (MIE) have been increasingly used and are regarded as suitable alternatives to open esophagectomy. However, few previous reports described minimally invasive esophagectomy using a left-sided approach. PATIENT CONCERNS AND DIAGNOSES: A 71-year-old man was admitted to our hospital because of progressive dysphagia. Synchronous double primary thoracic esophageal and left lung cancers were considered before the operation. INTERVENTIONS AND OUTCOMES: A lobectomy and MIE, via a left video-assisted thoracoscopic approach, was performed. Preparation of a gastric conduit and an intra-abdominal lymphadenectomy were completed by laparoscopy and a cervical anastomosis was made. In addition, a cervical mediastinoscopy was performed to dissect the lymph nodes along the bilateral recurrent laryngeal nerves. No postoperative complications were observed. The patient achieved a favorable short-term outcome. LESSONS: This is the first report of a patient with synchronous esophageal and left lung cancers treated with minimally invasive resection via left thoracoscopy, laparoscopy, and cervical mediastinoscopy. Our results showed that the left MIE approach in combination with cervical mediastinoscopy is potentially most appropriate for some esophageal cancer patients, when the right MIE approach is not applicable in certain conditions.

The NISTmAb tryptic peptide spectral library for monoclonal antibody characterization.

We describe the creation of a mass spectral library composed of all identifiable spectra derived from the tryptic digest of the NISTmAb IgG1κ. The library is a unique reference spectral collection developed from over six million peptide-spectrum matches acquired by liquid chromatography-mass spectrometry (LC-MS) over a wide range of collision energy. Conventional one-dimensional (1D) LC-MS was used for various digestion conditions and 20- and 24-fraction two-dimensional (2D) LC-MS studies permitted in-depth analyses of single digests. Computer methods were developed for automated analysis of LC-MS isotopic clusters to determine the attributes for all ions detected in the 1D and 2D studies. The library contains a selection of over 12,600 high-quality tandem spectra of more than 3,300 peptide ions identified and validated by accurate mass, differential elution pattern, and expected peptide classes in peptide map experiments. These include a variety of biologically modified peptide spectra involving glycosylated, oxidized, deamidated, glycated, and N/C-terminal modified peptides, as well as artifacts. A complete glycation profile was obtained for the NISTmAb with spectra for 58% and 100% of all possible glycation sites in the heavy and light chains, respectively. The site-specific quantification of methionine oxidation in the protein is described. The utility of this reference library is demonstrated by the analysis of a commercial monoclonal antibody (adalimumab, Humira®), where 691 peptide ion spectra are identifiable in the constant regions, accounting for 60% coverage for both heavy and light chains. The NIST reference library platform may be used as a tool for facile identification of the primary sequence and post-translational modifications, as well as the recognition of LC-MS method-induced artifacts for human and recombinant IgG antibodies. Its development also provides a general method for creating comprehensive peptide libraries of individual proteins.

In-Depth Characterization and Spectral Library Building of Glycopeptides in the Tryptic Digest of a Monoclonal Antibody Using 1D and 2D LC-MS/MS.

This work presents a detailed analysis of glycopeptides produced in the tryptic digestion of an IgG1 reference material. Analysis was done by nanospray ESI LC-MS/MS over a wide range of HCD collision energies with both conventional 1D separation for various digestion conditions and a 20 fraction 2D-LC study of a single digest. An extended version of NIST-developed software for analysis of "shotgun" proteomics served to identify the glycopeptides from their precursor masses and product ions for peptides with up to three missed cleavages. A peptide with a single missed cleavage, TKPREEQYNSTYR, was dominant and led to the determination of almost all glycans reported in this study. The 2D studies found a total of 247 glycopeptide ions and 60 glycans of different masses, including 30 glycans found in the 1D studies. This significantly larger number of glycans than found in any other glycoanalysis of therapeutic glycoproteins is due to both the improved separation of sialylated versus asialylated species in the first (high-pH) dimension and the ability to inject large amounts of glycosylated peptides in the 2D studies. Systematic variations in retention with glycan size were also noted. Energy-dependent changes in HCD fragmentation confirmed the proposed glycan structures and led to a peak-annotated mass spectral library to aid the analysis of glycopeptides derived from IgG1 drugs.

A Description of the Clinical Proteomic Tumor Analysis Consortium (CPTAC) Common Data Analysis Pipeline.

The Clinical Proteomic Tumor Analysis Consortium (CPTAC) has produced large proteomics data sets from the mass spectrometric interrogation of tumor samples previously analyzed by The Cancer Genome Atlas (TCGA) program. The availability of the genomic and proteomic data is enabling proteogenomic study for both reference (i.e., contained in major sequence databases) and nonreference markers of cancer. The CPTAC laboratories have focused on colon, breast, and ovarian tissues in the first round of analyses; spectra from these data sets were produced from 2D liquid chromatography-tandem mass spectrometry analyses and represent deep coverage. To reduce the variability introduced by disparate data analysis platforms (e.g., software packages, versions, parameters, sequence databases, etc.), the CPTAC Common Data Analysis Platform (CDAP) was created. The CDAP produces both peptide-spectrum-match (PSM) reports and gene-level reports. The pipeline processes raw mass spectrometry data according to the following: (1) peak-picking and quantitative data extraction, (2) database searching, (3) gene-based protein parsimony, and (4) false-discovery rate-based filtering. The pipeline also produces localization scores for the phosphopeptide enrichment studies using the PhosphoRS program. Quantitative information for each of the data sets is specific to the sample processing, with PSM and protein reports containing the spectrum-level or gene-level ("rolled-up") precursor peak areas and spectral counts for label-free or reporter ion log-ratios for 4plex iTRAQ. The reports are available in simple tab-delimited formats and, for the PSM-reports, in mzIdentML. The goal of the CDAP is to provide standard, uniform reports for all of the CPTAC data to enable comparisons between different samples and cancer types as well as across the major omics fields.