Objective function based ranking method for selection of optimal beam angles in IMRT

We propose a novel method for the selection of optimal beam angles in Intensity Modulated Radiation Therapy (IMRT). The proposed approach uses an objective function based metric called “target-to-critical organ objective function ratio” to find out the optimal gantry angles. The beams are ranked based on this metric and are accordingly chosen for IMRT optimization. We have used the Pinnacle TPS (Philips Medical System V 16.2) for performing the IMRT optimization. In order to validate our approach, we have applied it in four clinical cases: Head and Neck, Lung, Abdomen and Prostate. Basically, for all clinical cases, two set of plans were created with same clinical objectives, namely Equal angle plan (EA Plan) and Suitable angle Plan (SA Plan). In the EA plans, the beam angles were placed in an equiangular manner starting from the gantry angle of 0°. In the corresponding SA plans, the beam angles were decided using the guidance provided by the algorithm. The reduction in OAR mean dose and max dose obtained in SA plans is about 3 to 16% and 3 to 15% respectively depending upon the treatment site while obtaining equal target coverage as compared to their EA counterparts. It takes approximately 15–25 min to find the optimal beam angles. The results obtained from the clinical cases indicate that the plan quality is considerably improved when the beam angles are optimized using the proposed method.     

Performance assessment of a new optimization system for robotic SBRT MLC-based plans

PurposeTo assess the performance of a new optimization system, VOLO, for CyberKnife MLC-based SBRT plans in comparison with the existing Sequential optimizer.MethodsMLC-plans were created for 25 SBRT cases (liver, prostate, pancreas and spine) using both VOLO and Sequential. Monitor units (MU), delivery time (DT), PTV coverage, conformity (nCI), dose gradient (R50%) and OAR doses were used for comparison and combined to obtain a mathematical score (MS) of plan quality for each solution. MS strength was validated by changing parameter weights and by a blinded clinical plan evaluation. The optimization times (OT) and the average segment areas (SA) were also compared.ResultsVOLO solutions offered significantly lower mean DT (−19%) and MU (−13%). OT were below 15 min for VOLO, whereas for Sequential, values spanned from 8 to 160 min. SAs were significantly larger for VOLO: on average 10 cm² versus 7 cm². VOLO optimized plans achieved a higher MS than Sequential for all tested parameter combinations. PTV coverage and OAR sparing were comparable for both groups of solutions. Although slight differences in R50% and nCI were found, the parameters most affecting MS were MU and DT. VOLO solutions were selected in 80% of cases by both physicians with 88% inter-observer agreement.ConclusionsThe good performance of the VOLO optimization system, together with the large reduction in OT, make it a useful tool to improve the efficiency of CK SBRT planning and delivery. The proposed methodology for comparing different planning solutions can be applied in other contexts.     

Photon beam energy dependent single-arc volumetric modulated arc optimization

PurposeThe purpose of this work was to present a new single-arc mixed photon (6&18MV) VMAT (SAMP) optimization framework that concurrently optimizes for two photon energies with corresponding partial arc lengths.Methods and materialsOwing to simultaneous optimization of energy dependent intensity maps and corresponding arc locations, the proposed model poses nonlinearity. Unique relaxation constraints based on McCormick approximations were introduced for linearization. Energy dependent intensity maps were then decomposed to generate apertures. Feasibility of the proposed framework was tested on a sample of ten prostate cancer cases with lateral separation ranging from 34 cm (case no.1) to 52 cm (case no.6). The SAMP plans were compared against single energy (6MV) VMAT (SE) plans through dose volume histograms (DVHs) and radiobiological parameters including normal tissue complication probability (NTCP) and equivalent uniform dose (EUD).ResultsThe contribution of higher energy photon beam optimized by the algorithm demonstrated an increase for cases with a lateral separation >40 cm. SAMP–VMAT notably improved bladder and rectum sparing in large size cases. Compared to single energy, SAMP–VMAT plans reduced bladder and rectum NTCP in cases with large lateral separation. With the exception of one case, SAMP–VMAT either improved or maintained femoral heads compared to SE–VMAT. SAMP–VMAT reduced the nontarget tissue integral dose in all ten cases.ConclusionsA single-arc VMAT optimization framework comprising mixed photon energy partial arcs was presented. Overall results underline the feasibility and potential of the proposed approach for improving OAR sparing in large size patients without compromising the target homogeneity and coverage.     

Crosstalk between intracellular and extracellular salicylic acid signaling events leading to long-distance spread of signals

It is well recognized that salicylic acid (SA) acts as a natural signaling molecule involved in both local and systemic plant defense responses upon attacks by pathogens. Recently, cellular SA receptors and a number of SA-related phloem-mobile signals were identified. Here, we compare the old and up-to-date concepts of plant defense signaling events involving SA. Finally, the crosstalk between intracellular and extracellular SA signaling events leading to long-distance spread of signals was outlined by focusing on the modes of both the short- and long-distance signaling events involving the actions of SA. For the above purpose, two distinct conceptual models for local SA perception and signaling mechanisms in the intracellular and extracellular paths (referred to as models i and ii, respectively) were proposed. In addition to two local SA perception models, we propose that the long-distance SA action could be attributed to three different modes, namely, (iii) local increase in SA followed by transport of SA and SA intermediates, (iv) systemic propagation of SA-derived signals with both chemical and electrical natures without direct movement of SA, and (v) integrated crosstalk allowing alternately repeated secondary signal propagation and biosynthesis of SA and/or conversion of inert SA intermediates to free SA finally contributing to the systemic spread of SA-derived signals. We review here that the long-distance SA signaling events (models iii–v), inevitably involve the mechanisms described in the local signaling models (models i and ii) as the key pieces of the crosstalk.     

Local spatial autocorrelation in biological variables

Spatial autocorrelation (SA) methods have recently been extended to include the detection of local spatial autocorrelation at individual sampling stations. We review the formulas for these statistics and report on the results of an extensive population-genetic simulation study we have published elsewhere to test the applicability of these methods in spatially distributed biological data. We find that most biological variables exhibit global SA, and that in such cases the methods proposed for testing the significance of local SA coefficients reject the null hypothesis excessively. When global SA is absent, permutational methods for testing significance yield reliable results. Although standard errors have been published for the local SA coefficients, their employment using an asymptotically normal approach leads to unreliable results; permutational methods are preferred. In addition to significance tests of suspected non-stationary localities, we can use these methods in an exploratory manner to find and identify hotspots (places with positive local SA) and coldspots (negative local SA) in a dataset. We illustrate the application of these methods in three biological examples from plant population biology, ecology and population genetics. The examples range from the study of single variables to the joint analysis of several variables and can lead to successful demographic and evolutionary inferences about the populations studied.     

Evaluation of plan quality improvements in PlanIQ-guided Autoplanning

AimPhilips recently integrated PlanIQ with Autoplan® in Pinnacle³ TPS (V16.2). The objective of the present work is to quantitatively demonstrate how this integration improves the plan quality.BackgroundPinnacle³ Autoplan® is the tool that generates the treatment plans with clinically acceptable plan quality with less manual intervention. In the recent past, a new tool called PlanIQ (Sun Nuclear Corp.) was introduced for a priori estimation of the best possible sparing of an organ at risk (OAR) for a given patient anatomy. Philips has recently integrated PlanIQ tool with Autoplan® for a seamless and efficient planning workflow.Materials and methodsWe have performed this evaluation in Pinnacle³ TPS (V.16.2) for the VMAT treatment technique. All plans were created using Varian True beam machine with the dual arc technique. Basically, we created two sets of VMAT plans using 6 MV photons. In the first set of VMAT plans (AP_RTOG), we used OAR goals from either RTOG guidelines to perform optimization using Autoplan®. Subsequently, we exported the same dataset to the PlanIQ system to perform feasibility analysis on the OAR goals. These newly obtained OAR goals from PlanIQ were used to generate the other set of plans (AP_PlanIQ plans). We compared the dosimetric results from these two sets of plans in five cases, such as brain, head & neck, lung, abdomen and prostate.ResultsWe compared the dosimetric results for AP_RTOG and AP_PlanIQ plans. We used RTOG guidelines to evaluate the plans and observed that while both sets of plans were meeting the RTOG guidelines in terms of OAR sparing, the AP_PlanIQ plans were significantly better in terms of OAR sparing as compared to AP_RTOG plans without any compromise in the target coverage.ConclusionThe results indicate that, although Autoplan helps achieve the user-defined goals without much manual intervention, the plan quality (OAR sparing) can be significantly improved without taking many iterative steps when PlanIQ suggested clinical goals are used in the Autoplan-based optimization.Advances in knowledgeAt present, there are no published material available about the efficacy of the integration of PlanIQ with Autoplanning®. In the present work, our objective is to evaluate the improvements in plan quality resulting from this integration.     

Feasibility and potential advantages using VMAT in SRS metastasis treatments

BackgroundUtilization of stereotactic radiosurgery (SRS) for brain metastases (BM) has become the technique of choice as opposed to whole brain radiation therapy (WBRT). The aim of this work is to evaluate the feasibility and potential benefits in terms of normal tissue (NT) and dose escalation of volumetric modulated arc therapy (VMAT) in SRS metastasis treatment. A VMAT optimization procedure has therefore been developed for internal dose scaling which minimizes planner dependence.Materials and methodsFive patient-plans incorporating treatment with frame-based SRS with dynamic conformal arc technique (DA) were re-planned for VMAT. The lesions selected were between 4–6 cm³. The same geometry used in the DA plans was maintained for the VMAT cases. A VMAT planning procedure was performed attempting to scale the dose in inner auxiliary volumes, and to explore the potential for dose scaling with this technique. Comparison of dose-volume histogram (DVH) parameters were obtained.ResultsVMAT allows a superior NT sparing plus conformity and dose scaling using the auxiliary volumes. The VMAT results were significantly superior in NT sparing, improving both the V₁₀ and V₁₂ values in all cases, with a 2–3 cm³ saving. In addition, VMAT improves the dose coverage D₉₅ by about 0.5 Gy. The objective of dose escalation was achieved with VMAT with an increment of the Dmean and the Dmedian of about 2 Gy.ConclusionsThis work shows a benefit of VMAT in SRS treatment with significant NT sparing. A VMAT optimization procedure, based on auxiliary inner volumes, has been developed, enabling internal dose escalation.     

Organ-specific (localized) synthesis of Ig light chain amyloid

Ig amyloidosis is usually a systemic disease with multisystem involvement. However, in a significant number of cases amyloid deposition is limited to one specific organ. It has not been determined if the Ig light chain (LC) amyloid precursor protein in localized amyloidosis is synthesized by circulating plasma cells with targeting of the amyloid fibril-forming process to one specific organ, or whether the synthesis of Ig LC and fibril formation occurs entirely as a localized process. In the present study local synthesis of an amyloid fibril precursor LC was investigated. Amyloid fibrils were isolated from a ureter that was obstructed by extensive infiltration of the wall with amyloid. Amino acid sequence analysis of the isolated fibril subunit protein proved it to be derived from a lambdaII Ig LC. Plasma cells within the lesion stained positively with labeled anti-lambda Ab and by in situ hybridization using an oligonucleotide probe specific for lambda-LC mRNA. RT-PCR of mRNA extracted from the tumor and direct DNA sequencing gave the nucleotide sequence coding specifically for the lambdaII amyloid subunit protein, thus confirming local synthesis of the LC protein.     

Critical Structure Sparing in Stereotactic Ablative Radiotherapy for Central Lung Lesions: Helical Tomotherapy vs. Volumetric Modulated Arc Therapy

Background

Helical tomotherapy (HT) and volumetric modulated arc therapy (VMAT) are both advanced techniques of delivering intensity-modulated radiotherapy (IMRT). Here, we conduct a study to compare HT and partial-arc VMAT in their ability to spare organs at risk (OARs) when stereotactic ablative radiotherapy (SABR) is delivered to treat centrally located early stage non-small-cell lung cancer or lung metastases.

Methods

12 patients with centrally located lung lesions were randomly chosen. HT, 2 & 8 arc (Smart Arc, Pinnacle v9.0) plans were generated to deliver 70 Gy in 10 fractions to the planning target volume (PTV). Target and OAR dose parameters were compared. Each technique’s ability to meet dose constraints was further investigated.

Results

HT and VMAT plans generated essentially equivalent PTV coverage and dose conformality indices, while a trend for improved dose homogeneity by increasing from 2 to 8 arcs was observed with VMAT. Increasing the number of arcs with VMAT also led to some improvement in OAR sparing. After normalizing to OAR dose constraints, HT was found to be superior to 2 or 8-arc VMAT for optimal OAR sparing (meeting all the dose constraints) (p = 0.0004). All dose constraints were met in HT plans. Increasing from 2 to 8 arcs could not help achieve optimal OAR sparing for 4 patients. 2/4 of them had 3 immediately adjacent structures.

Conclusion

HT appears to be superior to VMAT in OAR sparing mainly in cases which require conformal dose avoidance of multiple immediately adjacent OARs. For such cases, increasing the number of arcs in VMAT cannot significantly improve OAR sparing.     

Perturbation analysis of 4D dose distribution for scanned carbon-ion beam radiotherapy

PurposeTo evaluate the patients’ set-up error-induced perturbation effects on 4D dose distributions (4DDD) of range-adapted internal target volume-based (raITV) treatment plan using lung and liver 4DCT data sets.MethodsWe enrolled 20 patients with lung and liver cancer treated with respiratory-gated carbon-ion beam scanning therapy. PTVs were generated by adding a 2 mm range-adapted set-up margin on the raITVs. Set-up errors were simulated by shifting the beam isocenter in three translational directions of ±2 mm, ±4 mm, and ±6 mm. 4DDDs were calculated for both nominal and isocenter-shifted situations. Dose metrics of CTV dose coverage (D95) and normal tissue sparing were evaluated. Statistical significance with p < 0.01 was considered by Wilcoxon signed rank test.ResultsThe CTV dose coverage was more sensitive to set-up errors for lung cases than for liver cases, and more serious in superior-inferior direction. The sufficient CTV-D95 > 98% could be achieved with set-up errors less than ±2 mm in all shift directions both for lung and liver cases. With the increase of set-up error, the CTV dose coverage decreased gradually. The clinical criterial of CTV-D95 > 95% could not be fulfilled with set-up error reached to ±4 mm for lung cases, and ±6 mm for liver cases. OAR doses did not have a significant difference with each set-up error for both lung and liver cases.ConclusionsThe range-adapted set-up margin successfully prevented dose degradation of 4DDDs in the presence of the same magnitude of set-up error for raITV-based carbon-ion beam scanning therapy.     

Image 1D OMP sparse decomposition with modified fruit-fly optimization algorithm

The Fruit-fly optimization algorithm (FOA) is good at parallel search ability in the evolution process, but it traps in local optimum sometimes. Simulated Annealing (SA) algorithm accepts the second-optimum solution with Mrtropolis criterion so as to jump out of the local optimum. So, combined the advantages of two algorithms, modified FOA (FOA-SA) algorithm is presented in this paper. In FOA-SA, the smell concentration function is improved as well, so as to get the whole searching directions for fruit-fly. At the same time, in order to solve the problem of the computational complexity in image 2D sparse decomposition, image 1D orthogonal matching pursuit (OMP) algorithm with FOA-SA algorithm is implemented. Experimental results show that the convergence of FOA-SA is better than that in FOA, and the speed of image 1D sparse algorithm is 2.41 times faster than 2D for the 512 \(\times \) 512 image under the same conditions.     

Normal tissue sparing using different techniques for prostate irradiation

AimThe aim of this study was to investigate normal tissue sparing through dosimetric parameters of normal tissue volumes using different irradiation techniques for conventional (CFRT) and simultaneously integrated boost (SIB) schedules.BackgroundSeveral dose-escalation studies for localized prostate cancer (PCa) have shown advanced biochemical relapse-free (bRFS) rates and also better local control for higher total doses using either CFRT or SIB schedules. Besides the most important organs-at-risk, absorbed dose reduction of other surrounding normal tissues are also preferable. In order to analyse the normal tissue sparing, dosimetric parameters of different normal tissue volumes were examined.Materials and methodsTreatment plans for 15 high risk prostate cancer patients were created using RapidArc (RA), Sliding Window (SW) IMRT and 4-field box (3D-CRT) technique. In order to evaluate normal tissue sparing, the volume of pelvic region was divided into six normal tissue cylinders with 1 cm wall thickness, located in each other.ResultsAll plans met the criteria of target coverage (V95%>95%). All techniques provided the same results for OARs except 3D-CRT for rectum and bilateral femoral heads. The values of V5, V10 and V15 increased in cases which included RapidArc technique and decreased for V20 and V30.ConclusionsThe dosimetric parameters for the cylindrical normal tissue volumes show that using RapidArc technique gives equal or slightly better normal tissue sparing and SIB provided the same normal tissue sparing as CFRT planned with RapidArc.     

A combined steepest descent and genetic algorithm (SD/GA) approach for the optimization of solvation parameters

An accurate solvation model is essential for computer modeling of protein folding and other biomolecular self-assembly processes. Compared to explicit solvent models, implicit solvent models, such as the Poisson-Boltzmann (PB) with solvent accessible surface area model (PB/SA), offer a much faster speed—the most compelling reason for the popularity of these implicit solvent models. Since these implicit solvent models typically use empirical parameters, such as atomic radii and the surface tensions, an optimal fit of these parameters is crucial for the final accuracy of properties such as solvation free energy and folding free energy. In this paper, we proposed a combined approach, namely SD/GA, which takes the advantage of both local optimization with the steepest descent (SD), and global optimization with the genetic algorithm (GA), for parameters optimization in multi-dimensional space. The SD/GA method is then applied to the optimization of solvation parameters in the non-polar cavity term of the PB/SA model. The results show that the newly optimized parameters from SD/GA not only increase the accuracy in the solvation free energies for ～200 organic molecules, but also significantly improve the free energy landscape of a β-hairpin folding. The current SD/GA method can be readily applied to other multi-dimensional parameter space optimization as well.     

Optimization of batch and fed-batch bioreactors using simulated annealing

In order for biobased industrial products to compete economically with petroleum-derived products, significant reduction in their processing cost is necessary. Since most bioprocesses are operated in batch or fed-batch mode, their optimization involves theoretical and computational challenges. Simulated annealing (SA), a stochastic optimization algorithm, is used in this study to solve a number of challenging optimization problems related to the design and operation of bioreactors. Two well-known case studies are considered in which the robustness and efficiency of the SA algorithm is demonstrated. More specifically, in the first case study it is shown that the global optimal solution located by SA achieves significant improved productivity when compared with the results of previous investigations. In the second case study a realistic objective function is considered where the economic performance of a bioprocess is optimized. SA exhibits impeccable performance and robustness and was able to locate the global optimal solution irrespective of the initial point selected.     

Tumorigenicity testing of primate cell lines in nude mice, muscle organ culture and for colony formation in soft agarose

Primate neoplastic and finite cell lines were tested in one in vivo and two in vitro test systems: adult nude mice, muscle organ culture (MOC) and soft agarose (SA). Comparison of the sensitivity of the systems indicated that nude mice were inferior to either in vitro system: WI-38 VA13 (an SV40 transformed cell line) did not cause tumours in these animals yet it behaved as if it were neoplastic in MOC and formed colonies in SA. There was complete correlation between results obtained in MOC and SA. All cell lines which produced tumors in vivo were positive in both in vitro test systems. None of the lines which showed normal patterns in MOC and in SA was tumorigenic in nude mice. Since testing in vitro is simpler, faster, and is thought to be reliable, we recommend SA followed by MOC as the initial assays for determining tumorigenicity of cells.     

A rapid heuristic algorithm for finding minimum evolution trees

The minimum sum of branch lengths (S), or the minimum evolution (ME) principle, has been shown to be a good optimization criterion in phylogenetic inference. Unfortunately, the number of topologies to be analyzed is computationally prohibitive when a large number of taxa are involved. Therefore, simplified, heuristic methods, such as the neighbor-joining (NJ) method, are usually employed instead. The NJ method analyzes only a small number of trees (compared with the size of the entire search space); so, the tree obtained may not be the ME tree (for which the S value is minimum over the entire search space). Different compromises between very restrictive and exhaustive search spaces have been proposed recently. In particular, the "stepwise algorithm" (SA) utilizes what is known in computer science as the "beam search," whereas the NJ method employs a "greedy search." SA is virtually guaranteed to find the ME trees while being much faster than exhaustive search algorithms. In this study we propose an even faster method for finding the ME tree. The new algorithm adjusts its search exhaustiveness (from greedy to complete) according to the statistical reliability of the tree node being reconstructed. It is also virtually guaranteed to find the ME tree. The performances and computational efficiencies of ME, SA, NJ, and our new method were compared in extensive simulation studies. The new algorithm was found to perform practically as well as the SA (and, therefore, ME) methods and slightly better than the NJ method. For searching for the globally optimal ME tree, the new algorithm is significantly faster than existing ones, thus making it relatively practical for obtaining all trees with an S value equal to or smaller than that of the NJ tree, even when a large number of taxa is involved.     

Variance-based sensitivity analysis of biological uncertainties in carbon ion therapy

PurposeBiological models to estimate the relative biological effectiveness (RBE) or the equivalent dose in 2 Gy fractions (EQD2) are needed for treatment planning and plan evaluation in carbon ion therapy. We present a model-independent, Monte Carlo based sensitivity analysis (SA) approach to quantify the impact of different uncertainties on the biological models.Methods and materialsThe Monte Carlo based SA is used for the evaluation of variations in biological parameters. The key property of this SA is the high number of simulation runs, each with randomized input parameters, allowing for a statistical variance-based ranking of the input variations. The potential of this SA is shown in a simplified one-dimensional treatment plan optimization. Physical properties of carbon ion beams (e.g. fragmentation) are simulated using the Monte Carlo code FLUKA. To estimate biological effects of ion beams compared to X-rays, we use the Local Effect Model (LEM) in the framework of the linear-quadratic (LQ) model. Currently, only uncertainties in the output of the biological models are taken into account.Results/conclusionsThe presented SA is suitable for evaluation of the impact of variations in biological parameters. Major advantages are the possibility to access and display the sensitivity of the evaluated quantity on several parameter variations at the same time. Main challenges for later use in three-dimensional treatment plan evaluation are computational time and memory usage. The presented SA can be performed with any analytical or numerical function and hence be applied to any biological model used in carbon ion therapy.     

Range optimization for target and organs at risk in dynamic adaptive passive scattering proton beam therapy – A proof of concept

PurposeThe purpose of this study was to design and develop a new range optimization for target and organs at risk (OARs) in dynamic adaptive proton beam therapy (PBT).MethodsThe new range optimization for target and OARs (RO-TO) was optimized to maintain target dose coverage but not to increase the dose exposure of OARs, while the other procedure, range optimization for target (RO-T), only focused on target dose coverage. A retrospective analysis of a patient who received PBT for abdominal lymph node metastases was performed to show the effectiveness of our new approach. The original plan (OP), which had a total dose of 60 Gy (relative biological effectiveness; RBE), was generated using six treatment fields. Bone-based registration (BR) and tumor-based registration (TR) were performed on each pretreatment daily CT image dataset acquired once every four fractions, to align the isocenter.ResultsBoth range adaptive approaches achieved better coverage (D_95%) and homogeneity (D_5%−D_95%) than BR and TR only. However, RO-T showed the greatest increases in D_2cc and D_mean values of the small intestine and stomach and exceeded the limitations of dose exposure for those OARs. RO-TO showed comparable or superior dose sparing compared with the OP for all OARs.ConclusionsOur results suggest that BR and TR alone may reduce target dose coverage, and that RO-T may increase the dose exposure to the OARs. RO-TO may achieve the planned dose delivery to the target and OARs more efficiently than the OP. The technique requires testing on a large clinical dataset.     

MALDI/MS peptide mass fingerprinting for proteome analysis: identification of hydrophobic proteins attached to eucaryote keratinocyte cytoplasmic membrane using different matrices in concert

BACKGROUND: MALDI-TOF-MS has become an important analytical tool in the identification of proteins and evaluation of their role in biological processes. A typical protocol consists of sample purification, separation of proteins by 2D-PAGE, enzymatic digestion and identification of proteins by peptide mass fingerprint. Unfortunately, this approach is not appropriate for the identification of membrane or low or high pI proteins. An alternative technique uses 1D-PAGE, which results in a mixture of proteins in each gel band. The direct analysis of the proteolytic digestion of this mixture is often problematic because of poor peptide detection and consequent poor sequence coverage in databases. Sequence coverage can be improved through the combination of several matrices. RESULTS: The aim of this study was to trust the MALDI analysis of complex biological samples, in order to identify proteins that interact with the membrane network of keratinocytes. Peptides obtained from protein trypsin digestions may have either hydrophobic or hydrophilic sections, in which case, the direct analysis of such a mixture by MALDI does not allow desorbing of all peptides. In this work, MALDI/MS experiments were thus performed using four different matrices in concert. The data were analysed with three algorithms in order to test each of them. We observed that the use of at least two matrices in concert leads to a twofold increase of the coverage of each protein. Considering data obtained in this study, we recommend the use of HCCA in concert with the SA matrix in order to obtain a good coverage of hydrophilic proteins, and DHB in concert with the SA matrix to obtain a good coverage of hydrophobic proteins. CONCLUSION: In this work, experiments were performed directly on complex biological samples, in order to see systematic comparison between different matrices for real-life samples and to show a correlation that will be applicable to similar studies. When 1D gel is needed, each band may contain a great number of proteins, each present in small amounts. To improve the proteins coverage, we have performed experiments with some matrices in concert. These experiments enabled reliable identification of proteins, without the use of Nanospray MS/MS experiments.